A huge turtle-shapes mecha, the "Turtleking" attacks a uranium storage facility. The ISO and the delegates of various countries are very concerned. Nambu, the only person who previously knew of Galactor, now officially anounces the existence of both the criminal organization "Galactor", as well as the Science Ninja Team that has been formed to resist them. The Science Ninja Team receives Nambu's orders, unites in the God Phoenix, and flies off right away to a missile launching base where the mecha was sighted. Ken stops Joe, who's eager to get into his first real fight. Ken takes Jun along and they sneak inside the mecha. With Ken's help the God Phoenix then enters the mecha and Joe, Jinpei and Ryu join the battle against the Galactor members. Elsewhere, the commander of the mecha tells Berg Katse of the Science Ninja Team's existence. Katse then relays the message to Governor X. In accordance with X's instructions, Katse orders the Science Ninja Team to be destroyed. The order is to have the mecha make a suicidal plunge, taking the God Phoenix with it, thus burying the Science Ninja Team. But at the very last moment, the God Phoenix escapes the mecha by using the Firebird Effect.

A spaceship disappears, along with a device that can report and record the location of the Earth's resources. The Science Ninja Team receives Nambu's instructions and heads towards the bottom of the sea, in the vicinity of the spot where contact with the spaceship was lost. There, prawn-shaped bulldozers leave a huge aircraft carrier located on the sea bottom to build a uranium factory. Ken stops Ryu who wants to fire a Bird Missile, and sneaks into the aircraft carrier alone. Ken discovers the spaceship's capsule inside the aircraft carrier, but the astronauts have been taken hostage. Ken is caught then too. In reality however, the pilots have already been murdered. Showing them as if they were still alive has been a trap. Jinpei has sneaked into the aircraft carrier following Ken on Joe's orders. He is able to rescue Ken as he is being led underground. The two of them collect the device and escape, destroying the computer in the aircraft carrier. The commander of the carrier gets blamed by Katse, and he gets into the head of the Turtleking to hurl himself at the God Phoenix. But due to Ken's quick thinking, the God Phoenix becomes the Firebird and the flames consume everything.

Deadly crashes involving passenger planes keep happening. Ken, who's investigating these occurrences, encounters a boy named Makoto. The boy is awaiting the return of his father who was reported missing in one of the accidents. Makoto's father is the younger brother of the inventor of Uranless, Dr. Takahara. The string of plane crashes has been caused by Galactor. They are intent on getting the Uranless, since it is capable of neutralizing the means of propulsion of their giant mummy. Ken has encountered the mummy in his Cessna before, and because of that incident, he has data concerning the propulsion system of the mummy. He contacts Dr. Takahara in order to get the Uranless. He meets Makoto's father, who miraculously survived the crash. But it's Katse in disguise. Katse battles with Ken and escapes. Makoto blames Ken for torturing his father and Ken promises him to bring back his father whereupon he gets the pin hiding the Uranless. The giant mummy appears at the airport and Ken is able to defeat it by firing the Uranless into it. But Makoto watches Katse, still in the guise of his father, flee in an escape rocket. He accuses Ken of breaking his promise to bring his father back. Ken accepts Makoto's hate silently since he lost his father ten years before in a similar way and has had the same thoughts - namely that his father would return some day.

During the investigation of an incident, Ken visits the Institute for Earthquake Research. Because of an earthquake caused by a mecha, he falls along with the director of the institute, into a crevice in the earth. Ken transmutes and is saved, but he cannot rescue the director. Ken stands before the director's grave and is attacked by the director's daughter Naomi, who firmly believes he's Galactor. Ken understands her anger at not being able to avenge her father and decides to let her know about his true identity as member of the Science Ninja Team. Consequently, he lets her join the team on the mission. In an investigation it has been calculated which resources the mecha will most likely attack next, and the God Phoenix encounters the mecha there. Inside, Ken wants to let Naomi avenge her father and asks Nambu for permission to fire the bird missiles. Nambu doesn't give permission, but Ken ignores him and tells Naomi to fire the bird missiles anyway. Naomi hesitates to press the firing button, and Ken takes Naomi's hand and makes her fire the missiles. At the director's grave, Ken hands his bracelet to Nambu. He says he wants to take the responsibility for making Naomi press the firing button without permission and resign from the team. However, Nambu says that Ken is needed for world peace and Naomi promises not to reveal his true identity.

Oceangoing ships from the ISO keep disappearing. It always happens in the vicinity of a place called "Cemetery of the Sea". Director Anderson and Nambu ask the Science Ninja Team to go to a base on the ocean floor which is most likely to be struck next. The Science Ninja Team gets Nambu's message and takes the God Phoenix towards the base at the bottom of the sea. Then they encounter a mysterious submarine, which leads them to the Cemetery of the Sea, where they see countless sunken ships. But when Joe says that all the ships are actually battleships, Ken gets suspicious and has the God Phoenix surface. There's fog everywhere on the surface. From the middle of the fog, a ghost fleet attacks them, but the Science Ninja Team guess correctly that the fog is man-made. They destroy the device creating the fog, but from the ghost fleet appear countless disks which attack them using light rays. The Science Ninja Team has to fight a hard battle. Just when all the missiles are used up and they don't know what to do, three red planes appear and shoot down the enemy machines using superior flying techniques. The commander of the fighter plane unit introduces himself to the baffled Science Ninja Team as "Red Impulse". He then flies away, leaving the words "We'll meet again" behind.

Gold bars are stolen from the vault of the World Bank. It is the deed of Galactor's Mini Robots. The Science Ninja Team get their instructions and start a search on the islands in the vicinity of the place where the gold bars seem to have been taken. Joe makes sure that Ken, Jun and Jinpei, in civilian wear, attract the enemy's attention and get taken off to the base. He proposes that if this is the headquarters, it should be destroyed right away. However, Nambu stops him by saying it's not the Science Ninja Team's duty to attack. Joe leaves a bored Ryu behind in the God Phoenix on the bottom of the sea and sneaks into the base in order to prepare for retaking of the gold bars. While Ken and the other create a lot of confusion in the interior of the base, Joe goes looking for the gold bars. He learns that a missile is about to be fired at the God Phoenix when it is detected by the surveillance cameras. He contacts Ryu in the God Phoenix, right away. Ryu, who is always merely on stand-by, is taking a nap, though manages to evade the missile by a hair's breadth. With Joe's guidance they store the stolen gold bars in the God Phoenix's interior. Ken and the others are contacted and escape from the base. The Galactor base and all its inhabitants are blown up because they didn't manage to prevent the gold bars being stolen back.

There's a new kind of plane that does not pollute the environment. In the middle of Ken's test flight of this ISO-developed plane, he is attacked by a biplane, piloted by a man who introduces himself as "Katzen Berig". Katzen Berig lashes with his whip at the ISO plane, causing it to crash, but Ken saves himself just in time by deploying a parachute. Nambu suspects from the name that Galactor is involved and orders the God Phoenix to attack immediately, but the God Phoenix's tailfin gets damaged by the whip. Analysis of the material stuck in the hull of the God Phoenix reveals that this kind of metal, called "super metal whisker", is something that has been researched by the ISO, but not manufactured. Nambu is taken aback at the scientific power of Galactor, but when the production factory is discovered, he gives the Science Ninja Team the order to destroy it. While the Science Ninja Team conducts a search with the God Phoenix in a mining area, they detect a huge mine. When they discover that this is where Galactor's secret factory is located, they sneak into it. By the end of the battle, they have succeeded in destroying the computer and the nuclear reactor. They try to make their getaway in the God Phoenix, but are caught by the strong magnetic attraction of the mine. They switch to jet propulsion and escape by a hair's breadth, leaving the exploding factory behind them.

A secret base. In order to resist their terrible enemy, Nambu thinks about a base for the Science Ninja Team. But fearing enemy intervention, he gives the Ninja Team orders to fly a patrol at Point G in the southern Pacific Ocean. Following orders not to intervene there, the God Phoenix leaves a smoke screen and flees when it encounters a sea anemone mecha. That night, Jinpei is with the other four team members, but he is not tired at all. He takes the G-4 and dives to the bottom of the sea. Children in the park had told him that G-4's popularity is the lowest of all the team members, and he intends on gaining their favour by being the best. Despite the worries of the other team members, he wanders around the sea bottom searching for the mecha. He never notices that he is being tailed by the mecha he seeks. Jinpei finds what seems to be a base under construction, but is caught by the mecha. He contacts Ken, but the base is blown up before his eyes. The mecha is destroyed by the God Phoenix and Katse gets away again. Jinpei wails that the base has been blown up because of his own egoistic actions, but Nambu tells him that the destroyed base was only a decoy. The Science Ninja Team had been the bait to attract the enemy's attention. The God Phoenix is flying high in the sky. Deep below stretches a crescent shaped coral reef. Below the reef hides the base which is capable of changing its location.

In the deep black sky the blue-white moon is shining. Suddenly, a meteorite falls down to Earth. According to analysis, the meteorite has the same composition as the moon. So Ken proposes approaching the moon in the God Phoenix to investigate. Approaching the moon, the God Phoenix encounters a swarm of meteorites heading for Earth. Ken discovers a wrapped up body in the middle of the swarm and, because this is not a meteorite he attacks. But the Bird Missiles have no effect. The body falls to the Earth, becomes a Scorpion Mecha and attacks an oil refinery. Following Nambu's instructions from Earth to find the source of the radio waves steering the mecha and the meteorites, Ken asks Jun to trace the signal they detected while the mecha was on its way to Earth. The Science Ninja Team find the carrier sending out the control signal and leave Ryu behind in the God Phoenix while they sneak into it. They question the commander, but he doesn't reveal anything. Joe loses his patience and fires carelessly into the control panels with a machine gun. Shortly after the Science Ninja Team escapes, the meteorites hit the carrier because the computer has been destroyed. Meanwhile on Earth, the Red Impulse squad reports that the now unguided scorpion mecha has been destroyed.

Suddenly, a whole city has lost power. Ken, in his Cessna, is thinking about an anomaly in the power plant when he gets a message from Nambu that the nuclear power plant has been attacked by a large group of ants. The Science Ninja Team goes to the site in question, but since the missiles would have hardly any effect on the tiny groups, they wash them away by breaking a nearby dam and using the force of the water. Upon analysing an ant they brought back, they learn that it's a finely and precisely manufactured robot. The robot ant gets repaired and, following its control signal, returns to its base. It is followed by Ryu in the God Phoenix in the sky and by the other four on the ground. They soon discover huge ant-hills, and end up in a huge ant cave when they try to sneak in. Katse is waiting for them where they fall and captures them in a dome made of reinforced glas. The air is about to run out and they don't know what to do, but in the end barely escape by using a bomb. In the meantime, swarms of ants have attacked the streets, but the Red Impulse squad exterminates them with flamethrowers. At this time, Katse lets a huge ant mecha take off. Red Impulse and the God Phoenix drive the ant mecha into an underwater tunnel. Collecting the sunlight with a mirror built into its nose, the God Phoenix burns everything with a strong heat ray. But Katse gets away again.

While flying, Ken is surprised to encounter the plane of the Red Impulse commander. He pursues him, but Red Impulse gets away using some superb flying technique; Ken longs to be able to use similar techniques. The Science Ninja Team gets order to guard the super powerful plane "Blue Hawk", pride of the country Toritan. But the crew of the plane has been killed before take-off and has been replaced with Galactor members. Nambu learns of this situation after take-off. He mobilizes Red Impulse in order to protect the Science Ninja Team from the Blue Hawk, since it is more powerful than the God Phoenix. The God Phoenix continues to accompany the Blue Hawk without knowing the situation onboard. Red Impulse appears, attacking the Blue Hawk and, after shooting a timebomb into it, disappears again. Ken sees that and firmly believes that Red Impulse is actually an enemy. Ignoring Nambu who wants to stop him, he pursues Red Impulse alone in the G-1. While Ken is away, the other four members get abducted and taken to a base located in a volcano. Ken however follows Red Impulse, who in turn is following the signal emitted by the time bomb. They arrive together and save the team just before they're executed. Nambu tells them that Red Impulse is a friend battling on their side. The G-1 and the Red Impulse plane fly through the sky wing-to-wing, reminiscent of bird parents flying with their children. Nobody at the time knows the meaning of the tear appearing in the Red Impulse commander's eye.

The world's raw material for sugar gets stolen by the Galactor mecha Ibukuron, and the world emergency sugar is getting very low. Ryu and Jinpei rush out into the street to buy candies. Just then, they get the order from Nambu to move out in order to follow Ibukuron and find the secret base. During the pursuit, the God Phoenix gets drawn toward the mecha by its strong magnetic force it uses to suck in the raw materials. Ken uses this force to sneak into the interior of the mecha, along with Joe and Ryu. However, the interior turns out to be a sugar factory and the three team members get sucked into the production process. They almost fall into a huge cooking pot filled with seething raw material, but somehow manage to escape. But then they enter a centrifuge and are rendered completely helpless. Meanwhile, Ibukuron has arrived at the base in a snow mountain and Jun and Jinpei sneak into its nuclear energy chamber. They turn off the power source, but get caught by the enemy. With the power turned off, Ken and the others can escape and arrive to rescue them. Just before escaping, Jun installs a time bomb and, as a result, the base disappears in the middle of an avalanche. The Science Ninja Team distributes the sugar, which they won back from Ibukuron, in a park. The children are now happy again.

A ISO constructed storage lake, which is part of a plan to make the desert fertile, disappears. The Science Ninja Team flies to Africa to investigate. An Elder there tells them the legend of the moving red sand. It is said that the red sand burns forever and that it can make civilisations grow, as well as destroy them. Ken asks the Elder about the sand's secret, but the Elder doesn't tell anything. Jinpei, following the Elder who's about to get abducted by Galactor, finds a pendant. The red sand contained in its interior is sent to Nambu and the analysis reveals that it's a new sort of bacteria and also a previously undiscovered powerful energy source. It has a thousand times the force of uranium and, if water is added, splits up and causes a big explosion. Because Galactor is looking for the red sand, a lion ant mecha changes the lake's location via an underground channel. The God Phoenix dives deep underground, discovers the caves used by the mecha and sneaks into the base they discover. But Galactor learns of the Science Ninja Team's arrival and they shoot the Elder after he reveals the secret. They head to the location where the red sand is locked up, one step ahead of the Science Ninja Team. Before dying, the Elder tells the Science Ninja Team the location as well. The God Phoenix gets there too late, the red sand is already stolen by the mecha. As a last resort, the God Phoenix turns toward the mecha as the Fiery Phoenix. As the red sand is touched by the flames, Galactor's high ambitions are burned, together with the sand.

It is reported that all kind of nuclear ships (cruise ships, submarines, battle ships etc) are disappearing. It is the deed of the Galactor mecha Icecander, aiming at nuclear energy. While investigating these incidents, the Science Ninja Team gets a message that a suspicious iceberg is moving forward against the current of the sea. The God Phoenix follows the iceberg, going to the north pole, where they discover a base in the middle of icebergs. Ken and Jun sneak into the base. In the base, while they are trying to take out the nuclear reactor, an operation is performed, designed to convert the crew and the passengers of the ships into Galactor members. With this strategy, Galactor wants to gain nuclear energy AND new members at the same time. Just at this moment, Katse wants to perform the operation on a small girl, passenger on one of the cruise ships. Ken and Jun invade the room and stop the operation, but Katse locks them up and leaves a time bomb in the room. In this instance, an old man in a wheelchair, who was on the same ship as the little girl, takes the time bomb in his arms and sacrifices himself, saving the others from the explosion. Ken and the others exit the operation room. First they free the abducted passengers and let them get back on board, then they blow up the base and escape. The Icecander pursues them, but the God Phoenix encounters it using the fiery phoenix and the mecha goes up in flames.

The town "Ghost City" has been destroyed 10 years earlier by environmental pollution. Communication with an investigation team sending data from there is lost. The Science Ninja Team goes there in the God Phoenix, which uses a soft skin (membrane) to protect it against the pollution. But as soon as they enter the city, they meet a Galactor attack. As it turns out, there's a base here. Nambu orders the U.N. military forces to attack. It seems everything is cleared after the attack. In reality however, a jellyfish lens created by Sosai X continues to grow at the bottom of the sea near the city. It uses the polluted sea water as its amniotic fluid. After finishing its growth, the jellyfish lens which turns the sunlight into energy a few hundred times stronger, completely destroys fighter planes from the U.N. forces. It then starts to attack the cities on earth. The God Phoenix dives into the sea near the city and discovers the base and the hiding jellyfish lense. They attack with missiles, but even though they destroy the base, the jellyfish lense flies out of the sea, pursuing the God Phoenix. The membrane protecting the God Phoenix is peeled off and puts it in a difficult situation. Just then, the Red Impulse group gets Nambu's instructions that in order to dissipate the poisonous gas the jellyfish lense breathes, they should throw high pressure oxygen at it. Protected by the Red Impulse machines, Ken flies they fiery phoenix into the jellyfish lense. The high pressure oxygen goes up in flames and the jellyfish lense burns to ashes on the surface of the sea.

The latest ISO weapon factory is used by Galactor and manufactures Mekanika. It's a machine which, according to the plan on a microfilm, can change its form constantly. The Science Ninja Team follows Mekanika. But when they lose sight of it, they continue searching individually before meeting in Nambu's house. While searching a tunnel where they lost sight of Mekanika, Jinpei discovers a base through a hole in the surface and sneaks into it. While trying to destroy the base, he finds a micro cassette. Judging from the behaviour of the Galactor members, this cassette seems to be very important and Jinpei takes it with him while fleeing. It contains the plans needed to change the form of Mekanika. Nambu makes a new plan, based off the cassette, and instructs the Science Ninja Team how to install this plan in Mekanika. As Mekanika transforms, there's a chink between the different parts of the casing. Ken sneaks into Mekanika through one of those chinks and wants to insert Nambu's cassette into the computer, but gets into a melee with Katse who was in the pilot's seat. Ken dives under Katse's arm and somehow manages to insert the cassette. Mekanika, according to Nambu's plan, transforms into a fair. When Katse sees that, he flees.

X, intending on using the strong destructive tendencies of humans, especially children, releases Kabutoron in the city. It destroys things using the children's brain waves. The children are happy when they find big stag beetles in one of the open areas, something which rarely happens in town. Also Jinpei finds one of the bugs and brings it home. In that night, each of the children's stag beetles grow large and they pull the children inside their bodies, fly out the room and start to destroy the city. While flying, Ken discovers how Kabutoron attacks a nuclear plant. But since Jinpei is missing, the God Phoenix cannot take off. Ken transmutes into his G1 plane and uses his X-ray on Kabutoron. Because he sees a child in the interior, he ceases to attack. The four members of the Science Ninja Team shadow Kabutoron and discover a base hidden in an ancient ruin. In the interior of the base, an operation intending to remove the children's brain and install them into Kabutoron is about to begin. A drill is just touching Jinpei's head when he's saved by a hair's breadth by Ken and Jun. They save the other children with Joe's help. Ken and the others get into the God Phoenix. Bombed by Red Impulse, Kabutoron blows up together with the base.

A huge whale keeps attacking harbours. While investigating a group of whales, the Science Ninja Team discovers a huge whale heading for this group. The huge whales fires a rocket aiming for the God Phoenix and flees, pushing aside the other whales. In reality, it's a Galactor submarine camouflaged as a whale. They want to follow the huge whale submarine, but, in order to save a young whale under attack by orcas, the G4 flies away. During all this, the submarine gets away. Nambu reproves them because of their squeamishness and puts a transmitter on the small whale so that he can help in the search for the big whale. The God Phoenix goes to the Arctic Circle, following the small whale. In order to search for the base, Ken and Joe leave the God Phoenix and encounter two men who introduce themselves as forest-keepers, but are then attacked from behind. Ken is baffled. Joe says that this is Galactor's trick and that his parents got murdered by the very same trick. The Science Ninja Team discovers the base and sneaks into it. They learn that a group of submarines is about to leave and attack the harbours in the world. They install explosives in the base and in the submarines. But, in order to help the little whale who ended up in the base, Jinpei dives with him into the sea. The Science Ninja Team can't stop the operation at this point, and escapes leaving Jinpei. But after the explosion of the base and the submarines, they are contacted by Jinpei, saying that he was saved by the small whale, and everybody is very relieved.

The Ruman Kingdom is known as the Gambling Kingdom. Galactor, guaranteeing the king's position, is channeling millions in riches out of the country. His highness Prince Luga's heart is torn by the people moaning with the high taxes imposed by the kingdom. So he contacts the ISO and offers to hand over a microfilm containing the location of the Galactor bases and headquarters to them. He does this knowing that it's against his father the king's, orders. In order to lay their hand son the film, the Science Ninja Team takes part in a race sponsored by the prince in which everybody can participate. But the encounter obstacles set by Galactor, who know the prince's plans. They're lured, together with the prince, into the base located in the interior of the kingdom. Katse wants to force them into exchanging the film against the king's life. But the prince has already handed over the film to Ken. Katse gets angry and shoots the king. The prince, clinging to his father's body, cries very much. But he has now his duty towards the people of the kingdom. Katse wants to take back the film by force. In order to achieve this wants to cut open Jinpei's stomach, since he pretended to swallow down the film. After the ensuing brawl, Joe has Katse cornered and is about to take away his mask, but Katse get away again by a hair's breadth. Despite the fact that they saved the prince's life, the film, which cost a huge sacrifice, was burned as well.

A Galactor mole mecha appears. The Science Ninja Team is contacted and starts to meet, but on the way there, Joe wants to save a small dog beside his mother, who was killed in the attack. Joe suffers a rocket attack. The mecha starts attacking the God Phoenix as well, but, since it gets weak in the sun, it has to withdraw at dawn. In the examination it becomes known that Joe got hit in the head by a fragment of the rocket. Since it's a very dangerous area an operation is impossible. Also the attempt in the high speed centrifuge fails. Then a message arrives saying that the mecha has appeared again. The other four members are mobilized, but their thoughts remain with Joe. But because the G2 car does not meet up with them, the God Phoenix cannot use its normal powers. At that moment, Joe appears in the G-2. He's taken immediately into the God Phoenix, but while they are still thinking about the reunion, they are caught in the mecha's hand. The God Phoenix wants to escape its certain doom, but it's impossible. Joe presses the firing button for the rockets and blows up the mole mecha. The God Phoenix is caught in the resulting shock wave and is thrown away rotating heavily, but with Ryu's steering capabilities they can recover. The resulting jolt gets the fragment out of Joe's head and he escapes alive.

A horse owned by a doctor who is an authority in the area of cyborgs, participates and wins with an astonishing performance at the world-famous horse grand prix. When Nambu sees this video, he guesses that this horse is a cyborg. He orders the Science Ninja Team to guard the Doctor so that his astonishing cyborg technique is not abused. But when Ken and the others arrive, it's already too late. Only one Galactor badge has been left behind and the Doctor has vanished. Dr. Henjinman has been brought to the base where he recognizes X's real face. He threatens X, saying that he will reveal his secret if he is not made X's representative. X reluctantly agrees. The Doctor's cyborg horses attack a meadow. The Science Ninja Team pursue them and sneak into the base. Inside, they find the doctor standing before X to reveal his face, just as he wanted. The doctor falls down as he's hit by a light rays projected by X when Katse pressed a button. Katse orders the horses to attack the city and flees. The Science Ninja Team escapes and blows up the base. Dying, the doctor tells them to press the buttons on the horses' backs. After the Science Ninja Teams has pressed the buttons on eac of the horses, he activates the self destruct mechanism of the horses and silently dies.

A uranium mining factory at the bottom of the sea is attacked by the mecha "Kingdragon". Since a guard vessel with much more power than the God Phoenix was beaten during the attack, Nambu does not order the Science Ninja Team deployed. But Ken disobeys Nambu's orders and goes to face the mecha in the God Phoenix. But the God Phoenix is no match against the enemy and even their trump card, the firebird, is beaten by the much higher temperatures. Nambu orders the Red Impulse group to attack the mecha, but the Red Impulse commander believes that Ken should face the enemy again and refuses Nambu's order. So Nambu comes up with another plan. He wants to install a cooling device in the God Phoenix, which is then supposed to react with a minus bomb to be installed in the interior of the mecha to freezing the enemy. Knowing this will be very dangerous, Ken applies for the job of installing the minus bomb. Hiding in a swarm of tuna, Ken sneaks into the mecha. He succeeds in placing the bomb, but he has no more time to escape as the mecha starts to freeze from the icy firebird. The Science Ninja Team is worried and wondering about Ken, when he suddenly appears in front of them from a crack in the mecha, like an immortal bird.

From the cellar of a bowling alley, the "Mecha Ball" appears and starts to destroy the city. Because of the Mecha Ball's simple structure, an attack is futile since there is no weak point. Opposing his four eager teammates, Ken decides not to go out, saying that if they attack without a chance for winning, they will only die a useless death. At the same time, Ken watches Jinpei move a pachinko ball with a magnet and gets an idea how to defeat the mecha. When Nambu hears Ken's proposal, he immediately builds a huge electrical magnet in the middle of the alps and decides that the God Phoenix must lure the mecha there. But with the mecha lured halfway to its destination, it changes its course to an international nuclear plant. Ken wants to get into the mecha himself and steer it towards the magnet. Joe wants to stop him, but Ken convinces him and flies away from the God Phoenix. Getting in the mecha alone, Ken defeats the Galactor members and changes the course of the mecha. He destroys the steering panel, making sure the course cannot be changed anymore. As Jun holds her breath and watches, the mecha ball is drawn towards the magnet and explodes. Ken's figure is reflected in the tear-filled eyes of the four teammates, similar to a bird flying in the sky.

Scientists from the ISO headquarters are murdered one after the other and Nambu orders the Science Ninja Team to act as bodyguards. The Science Ninja Team separate for their guard duty. During Ken's guard, he surprisingly meets Galactor's Ninja Blackbirds and follows them, but loses sight of them near an amusement park. At the same time, Jun and Jinpei are attacked by a Neon Giant which appeared accompanied by the sounds of a flute. In order to let the scientist escape, they offer themselves as bait, but fall off the street. Jun reports that the Neon Giant resembles the Indian statue standing before the amusement park where the Black Birds vanished. Because of that, the Science Ninja Team waits for the night and sneaks into the park to start investigating. Since Jun said that she heard the sounds of a flute, Ken follows a flutist who leads him into an underground base. It's Katse in disguise. Katse tells Ken that this night, Nambu will get attacked. Ken gets in contact with Joe and Ryu, telling them to hurry to Nambu's location, but he's caught in a pertinacious attack from the Black Birds. Before his eyes, Katse steers the Neon Giant with the flute's tune. When Jun and Jinpei intrude, Ken flings the flute away, and orders Jinpei to play on it. Through Jinpei's nonsensical tune, the Neon Giant overheats and explodes. The plan to asssasinate Nambu has failed.

An ISO volcanic research center is attacked. The God Phoenix, starting the investigation, is surprised by the Magma Giant and escapes into the sea where the Giant cannot follow it. When Joe says that the Magma Giant's face resembles the face of Jesus Christ sculptured into a steep slope in the national park, the Science Ninja Team goes there to investigate. A girl climbing the Jesus Christ sculpture is suspected to be a Galactor agent by Joe and questioned, but she answers that she's here to sculpture the statue, continuing the tradition of her family in the third generation. Together with the girl they go into the cave found in the steep slope and discover a base. The Jesus Christ face sculpted in the slope, is plunged into lava seething in the interior of the base and comes out as the Magma Giant. Seeing this, Ken calls the God Phoenix. At the top of the base, there's a special glas which is actually at the bottom of a sea. The sea is used as a lense to heat the magma, using the sunlight. With a rocket, they break the glas and thus destroy the base. When a message comes in from Nambu that the Magma Giant is heading towards a city, the Science Ninja Team split up in their individual machines and lure the Magma Giant towards the sea. The Magma Giant cannot resist and steps into the sea. Through the sea water he's instantly cooled and becomes a black piece of rock, standing still. The girl then gets her chisel to begin sculpting again.

ISO ships are attacked one after the other by Galactor's black ray. And because Ryu is napping in the God Phoenix, he cannot be mobilized. Ryu feels responsible and gives Nambu his bracelet back, while shaking off his teammates who want to stop him. He then goes back to the fishing-village where he was born. During this time the fishing areas in the village become polluted through unknown causes. Since Ryu's father is the co-operative head, is blamed by the village people. Ryu tells his father to ask Nambu to analyse the sea water. In the analysis, a matter is found which results from a process to produce metal. Nambu thinks it's Galactor's deed and arrives in the fishing village with the Science Ninja Team. Thinking that the sea is strange, Ryu, together with Ken who has been following him, discovers a machine in the water shaped like a ray, which can fly in the sky and dive in the sea. Following it, they discover a base and sneak into it, but end up getting caught. When they succed in barely escaping, Galactor is about to deploy the ray machines to attack the world. The two men lock themselves up in the command room and defeat Galactor by letting water flow into the base, but they wind up getting caught into the base themselves. Ken reports to Nambu that the destruction of the base has been accomplished by Ryu and requests that he be taken back into active service. The two men, waiting for their death, are rescued by the G4 machine. Back on surface, Ryu gets his bracelet back from Nambu.

The ISO gets a message from Lucy, one of the executives at Galactor, that she wants to reveal the location of their headquarters in exchange for $ 10 billion. Therefore they contact Lucy by having Joe team up with her in the world customer car endurance race across Africa. The other 4 team members are going to act as guards for their scout. After Joe gets into the car, he expects the information immediately, but Lucy says it's not possible until the rally is over. On the way, they are attacked by mechas camouflaged as animals. It is Galactor who have come to know of Lucy's treason. But with Ken and the other's help, they escape the attacks and continue the rally. As they approach the finish line, Lucy asks her old friend Joe whether they don't want to team up and take over Galactor. Evading all kind of obstacles, the team of Lucy and Joe wins the race and gets $ 100'000 in prize money. In the tea room, Joe demands that Lucy gives him the information as offered. When Lucy tries to answer, she suddenly starts to move strangely and finally breaks through a wall and falls to the ground where she explodes. She was a cyborg manufactured by Galactor, and a radio signal emitted by X caused her to self destruct. Joe is taken aback by Lucy who is now nothing more than a pile of iron fragments. His anger towards Galactor is ignited again.

Children keep dissolving into thin air. Even the members of the Science Ninja Team become eye witnesses to one of the disappearances. Ken follows some tire tracks on the ground and enters a mirror maze. There he discovers some snail mechas, but they become transparent and disappear. Galactor is collecting children with strong brain waves in order to produce the brain wave monster Alphagila. The monster reads the secrets of the ISO in its institutions, and then destroys them. Nambu enhances Jun's brain waves for a while and makes her pose as a bait. The Science Ninja Team locates her radio signal, sneaks into the base beneath the mirror maze and saves the children. Then, based on the information he got, Katse is going to an uranium storage room in the desert. But, because the interior of the room becomes a mirror dome, the mechas which snuck in and should be transparent, become visible. In reality, they fell into the trap Nambu prepared. The mechas are thrown aside by the fast-approaching God Phoenix. The Science Ninja Team thinks that they have cornered Katse for sure this time, but he gets away again, disappearing in blue-white flames.

Jinpei and Ryu visit the Shirayuki orphanage where Jinpei grew up, in order to play with friends. The children beg them to take them to watch some kickboxing. At the same time, in a volcanic area, strange things are happening. Ken and the other two go to investigate, but don't find anything extraordinary. After watching the fight, the children go to ask the winner, Galack X, for an autograph. They learn however that he was trained with deadly weapons in his boxing gloves. They are caught by the female assistant and taken away. Ryu, following Galack X by Jinpei's request, battles with Galack X, but gets hurt. He contacts Ken and the others. Jinpei, following the children, sneaks into a building behind the orphanage. There's a Galactor base and the assistant is Katse in disguise. Katse intends to have the now inactive volcano erupt and burn the city. Jinpei's clackers hit the switch and the eruption begins. Katse escapes in a rocket. With Ken and others, who had now arrived, they defeat Galack X and save the children. But the lava is flowing out of the mountain in direction of the city. Burning the orphanage, it continues its way. Despite his injuries, Ryu suddenly comes flying in the God Phoenix. They unite and destroy the mountain with a rocket, succeeding in damming up the lava. The city is saved, but the orphanage is completely burned. The Science Ninja Team starts to rebuild it, together with the children.

A water shortage is occurring everywhere. As if to pursue the beaten enemy, an invisible enemy continues to pound, destroying dams and water tanks. The Earth is put into a grave situation. The God Phoenix is mobilized and discovers the flying mecha Kamisoral which has become a white shadow. Merely flying past it causes great damage and missiles are useless since they can be cut apart by the mecha's sickle. The Science Ninja Team somehow manages to escape and report to Nambu. During this time, an announcement from Katse is received saying that tomorrow will be the last day for mankind. Nambu guesses that the Mecha will attack a nuclear power plant next. In order to create turbulences and a vacuum, which are regarded to be the mecha's weak point, a plan to create artificial rain is changed to the size of a typhoon. Equipped with a special filter, the God Phoenix goes to the power plant and succeeds to lure the mecha in the test area for the artificial rain fall. While waiting for the artificial typhoon, the God Phoenix is caught by the mecha and has to fight very hard. The missiles show no effect either and the God Phoenix, caught in the sickle of the mecha, is drawn into the typhoon together with it. In one instance, the force of the mecha's sickle is diminishes because of the thunderstorm's shock. The God Phoenix is able to escapes. The Mecha is drawn into the eye of the typhoon by the vacuum and explodes. The Earth's crisis is over.

Nambu's car is attacked by Galactor. But because of Joe, who seems to remember the Devil Star's rose bomb, they escape by a hair's breadth. Everybody wants to fully concentrate upon protecting Nambu since he's targeted. But Joe cannot agree with them and leaves the villa. In order to control his anger, Joe runs his car around a racetrack. When his parents were murdered, he too suffered a lethal wound by a rose bomb. His memories revive and he thinks of revenge. Just then, he has to save a woman from an accident on the track. Before parting, they make an appointment to race on the track together the following day. Meanwhile, Nambu boards the cross-continent train, along with Chief Anderson's secretary, in order to conduct an investigation. Ken thinks that it's a Galactor trap and boards the train too. The remaining three team members hide and wait for the Devil Stars in their individual machines. Ken defeats the Devil Star members in the train, but the secretary, having turned into the female commander manages to flee in a disc-shaped plane. Jun defeats the Devil Star members who want to destroy the tracks further ahead. Joe faces the last remaining Devil Star member. He knew the spot through a feather shuriken left by Ken in a map. Their respective weapons clash. The rose bomb pierces the Devil Star's chest along with the feather shuriken. They go past each other and behind Joe's back, the Devil Star's mask falls away. Her face is revealed to be the girl Joe was planning to race.

Galactor is targeting Lawnpark City, which the ISO has used all its resources to complete. The Mecha Gezora appears and starts to attack. The God Phoenix confronts it, but the mecha escapes through the use of a smoke screen. Receiving a warning from Galactor, the Science Ninja Team mixes with the other citizens and starts to investigate. But thinking this might be a Galactor trap, they take off their bracelets and split up in the city. While searching, Jun and Jinpei save a woman being attacked by violent criminals and get invited into a manor-house. Jun thinks all this is suspicious and accepts the invitation on purpose. The lady of the house ushers them inside and invites them to a delicious and abundant meal. Jinpei falls asleep because of a drug in the coffee, but Jun only pretended to drink and fall asleep. She watches what is going on carefully. When the lady of the house orders her men to kill them Jun offers resistance, but she gets caught. She excuses herself, saying that she's a a city police officer, but the lady of the house is convinced that she's part of the Science Ninja Team and locks both of them up in a subterranean prison. Ken and the others get worried when Jun and Jinpei don't show up at the agreed time and they split up again. Meanwhile, Gezora tries to lure the remaining three members of the Science Ninja team into the open by attacking a chemical factory.

The Science Ninja Team doesn't know where Jun and Jinpei are, and Gezora starts to attack. But with two of them missing, scoring is difficult for the team. Katse appears on the big city square and publicly announces that he will continue the attack until the Science Ninja Team shows itself. As the Galactor rifles are trained on some children throwing stones, Ken's boomerang comes flying in and Joe and Ryu also seize the opportunity to appear. Katse gets cornered, but boasts that two of the Science Ninja Team are his prisoners. Ken contradicts this statement, saying that the remaining two members are inside the God Phoenix. Katse gets into Gezora and flees. Jun and Jinpei are about to be executed by the lady of the house when, according to Ken's plan, the God Phoenix with five human figures in it passes on a screen. The execution is stopped. As Ken sneaks into a manor-house which appears suspicious to him, he finds a message saying that if he wants to save the two, he should come to the uranium storage building. The God Phoenix hurries there. There, Gezora is flying with the building in its hands. Ken sneaks into Gezora and saves the two team members. After Jun has installed a bomb, they escape together. The Science Ninja Team, again consisting of five members, shows itself and heads towards Katse. Gezora explodes when it touches the uranium, and again, Katse is the only one who gets away.

Strange radio waves attack people together with an aurora. Afterwards they run amuck and cause grave accidents. While fishing, Ryu is also bathed in these radio waves. Because Ryu's speech and behaviour are strange after he comes back to the base, an investigation is conducted. It results that Ryu's brain waves are like those of a cat. Additionally, Nambu is touched by those radio waves as well. In a rage, he tries to activate the switch for the self-destruct mechanism of Crescent Coral. Joe punches him out. Ken and Joe take Ryu with them and go to the place where Ryu got hit by the radio waves, in order to find clues. Because they can't get any answers, Joe gets angry and punches Ryu, who then hits the boat's panel and suffers an electrical shock. However, this causes him to return to his true personality. They think that an electrical shock might also work in Nambu's case, but because Nambu's brain waves keep changing their frequency, they have to destroy the mechanism producing the radio waves. The God Phoenix is therefore mobilised, and they seek the suspicious aurora Ryu saw. What they finally find is Thundersaurus, but the Science Ninja Team has to fight hard because the mecha's barrier of radio waves. A rocket is fired, but gets stuck and does not work. But as the mecha increases its electrical voltage, the blind shell explodes. Jun has made all the necessary installation to create the situation in which the increased voltage causes an explosion. The mecha is destroyed and all the people running amuck become their usual selves again.

In the country Doria, oil springs have been discovered. A battle has started between the King, keen on the mining rights, and the Prince, who's on the side of the poor, revolting people. It has become a civil war. Now there's also a never sleeping force, intent on making this into a world war. The King, in a disadvantageous situation in this war, asks the Science Ninja Team for help. The God Phoenix sneaks into the country in firebird mode. Ken contacts Prince Ali and convinces him to talk one more time with his father, the King. Together they go to the palace. But the King's answer is a volley of bullets, aimed at the prince and his companions. Ken stops the Prince who wants to attack the King. They both are dropped through a hole in the floor into a subterranean prison, where they find the skeleton of the true King. Ken tells the God Phoenix to come and get them, thus escaping. At the palace, people are gathering to demand the release of Prince Ali. The Mecha Moskon attacks them with bombs. Katse, disguised as the King, is chuckling while watching this. Ken appears before him and cuts the escape rope which Katse is holding. Katse falls into the city streets, which are wrapped in fire. Elsewhere, the Mecha's nature of following every move is uncovered and the God Phoenix is able to lure it into the oil field. The God Phoenix shoots it and it goes up in flames together with the oil field. The people of Dorian see the God Phoenix, coming out of the flames as firebird, and worshipping the Firebird God, they start to believe in the rebuilding of their country.

An ISO research ship is attacked and data regarding uranium resources on the bottom of the sea is lost along with it. In the middle of the investigation, the Science Ninja Team discovers three persons, a father and his two sons, floating on the sea. They say they witnessed the occurence while fishing. But in the village they live, the brothers Taro and Jiro and their father have the reputation of being liars. Nobody wants to listen to their testimony that they saw an apparition of a crawfish and a moving lighthouse. Ken discovers that the squid the family fished out is a rocket. The Science Ninja Team decides to have a look at the lighthouse. Ken saves Taro and his brother from a lynx in the vicinity of the lighthouse. They were imitating the Science Ninja Team by putting on capes made of chicken feathers. The Lynx turns out to be a Galactor cyborg. Then, Taro says that he knows a screct passage to the lighthouse and leads Ken there. Beneath the lighthouse, there's a Galactor base. In the ensuing confusion, Taro and Jiro board the lighthouse rocket which also holds the uranium resource data. The Galactor commander, thinking he captured the Science Ninja Team, goes to the base where Katse is waiting. The God Phoenix, following the crawfish mecha and is attacked by special metalic seaweed and rocket squids. In the vicinity of the attack, they discover the base. They rescue the children and recover the data. Katse, though cornered by the five team members, manages to escapes again by using a glas partition wall.

Dr. Miwa is researching whether the surface of the Sanjo Lake, frozen over the whole year, can be used to produce strong energy from the sun, instead of using polarization glas. Now he has gone missing. He had questions because this year the lake wasn't frozen over and seemed to have started an investigation. Nambu orders the Science Ninja Team to look for him since he fears the misuse of the Doctor's research, but also because the Doctor is his friend. The Science Ninja Team, led by the Doctor's pet Taro who was able to get to Nambu with a camera, heads towards the snowy mountains. There they discover a Galactor base. The Science Ninja Team and Taro are tricked by the Doctor's reflection. Taro is washed away by water falling from the ceiling of the base where the surface of the lake is located. The Science Ninja Team is locked up by walls made of reinforced glass. But with Taro's help the Science Ninja Team escapes and intervenes in the test area for the mecha using the Doctor's research. Ken's boomerang cuts through Katse's mask. Hiding his face, Katse flees. Ken, taking the Doctor with him, steals the enemy's snowmobiles and escapes from the base. Taro attacks the snowmobiles of the Galactor members about to assault the Doctor and the Doctor is saved, but Taro falls out of sight towards the bottom of the valley. Lenjira explodes because the Doctor is not present at the experiment. It disappears together with the base.

As part of the Mantle plan, a pollution-free city is constructed in the desert. Nambu and the Science Ninja Team have come into the city for the inauguration. In the middle of the parade, a man who introduces himself as the archaeologist Dr. Mukashiski is distributing leaflets for a dinosaur exhibition. That night, the city is attacked by dinosaurs, and Ken sneaks into the dinosaur exhibition from Dr. Mukashiski. It turns out to be a jungle from the dinosaur period. Ken is caught by ivy made of metal and can escape into a subterranean sewer, but his bracelet is taken away this time. The Doctor takes the bracelet and, in order to make this is own merit, hides it. Ken is severely scolded by Nambu who then orders the Science Ninja Team to get the bracelet back by all means. Nambu also leaves the attack on the dinosaurs to Red Impulse. Ken sneaks back into the sewer from which he escaped, and is discovered by the enemy, but G-4 followed him and saves him. Together they sneak into the base and rescue the three other team members who have been caught inside the base. They also recover the bracelet from Dr. Mukashiski. With the remote control destroyed by the Science Ninja Team, the magnetic propulsion energy of the dinosaurs explodes and they are destroyed along with the base.

Outside of Earth's atmosphere, a Devilstar ship appears. Spores of the Jigokiller plant are released towards Earth by Katse's hand. In a rainy night, women (and only women) are attacked. Jun who is alone in her shop, is attacked as well. She brings tissue of one of the flowers that was burned by her bomb, to Nambu. In the analysis, it results that it's a flesh-eating plant from ancient times. But it's not yet decided what its weak points, habits, etc are. Because only women are attacked, Jun simply borrows a protective suit which allows the bearer to breath also deep in the ocean and drives quickly through the city on her motorcycle, acting as a bait. Jinpei follows her, and she is swallowed by the Jigokiller plant in front of him. The Jigokiller flees. While looking for Jun, the Science Ninja Team receives orders to burn some Jigokiller plants to finish them off. They are located at a water reservoir that serves 10 million people. The team members hesitate since Jun may still be alive in one of those plants, but Ken says that it's the duty of the Science Ninja Team and even though he's grieving, drops his plane's fuel onto the flowers. Knowing Ken's feelings, the God Phoenix sets the flowers burning with a missiles. Meanwhile, Jun is caught in the interior of one of the flowers. The flames are stirred up, and from the interior of the flowers white spores are released, spores whose secret is yet unknown to the Science Ninja Team.

Jinpei is lost in mourning in Jun's empty shop. Elsewhere, Nambu is absorbed with the research on the Jigokiller plants. Hidden in the sewer, the Jigokiller plants start their activities and many damage reports follow. Ken refuses the order to move out, driven by the remorse that he abandoned Jun. Red Impulse beats into him the importance of the responsibility that it's up to him to at least find her body if Jun is dead. Ken's bracelet receives a bird scramble signal. Despite the fact that it might be a trap, the Science Ninja Team is mobilized. Willy City is well-equipped with sewers. They locate the bird scramble in a subterranean base. It is ideal for the Jigokiller plants, since they're weak in the sun and they grow in darkness and water. Breaking into the base, they are barely able to rescue Jun who is bound to a scaffold. Meanwhile, Nambu discovers by coincidence that his blood causes the Jigokiller plan to wither. Because of this, he finds out that the plant cannot stand the Y-chromosome that every man has. He entrusts Red Impulse with a special Y-chromosome bomb. Because of the bomb dropped by Red Impulse, a Y-Chromosome rain is falling and each of the Jigokiller plants wither. The crisis of humankind is over.

Invited by Jun, the Science Ninja Team visits a concert by the popular rock group Demon 5. The Demon 5 is kidnapped by Galactor right in front of them. Galactor has Demon 5 play the murder music composed by X. Using a Sonic Mecha, they start to play this music high above the city. The music destroys buildings and drives people crazy. The God Phoenix is mobilized, but meeting a counter-attack, it's forced to retreat for the time being. Revived by the operation's success, Katse has Demon 5 play another powerful murder music, but this time, the drummer uses his sticks to add a morse code signal. Jun notices this signal woven into the music. The analysis reveals that the signals tells the location of the Galactor base. Hurrying there in the God Phoenix, the Science Ninja Team saves Demon 5 just before their execution. But they are attacked by the Sonic Mecha. They get advice from Nambu that they should emit the same sounds, delayed by half a tact. As they follow this advice, the magnetic waves from the Sonic Mecha are interrupted and it self-destructs. Back home safely, the Demon 5 are in concert again. The Science Ninja Team is present as well, listening to the music as common people.

During his vacation, Ryu asks a passing car whether they can take him with them. But the car is part of a Galactor plan to free prisoners. Ryu is consequently captured by Galactor and taken along to the Jinjin prison which houses only prisoners sentenced to death that have tried to escape earlier. Galactor, upon arriving in the prison, kills the guards and has the prisoners assemble in the prison yard. The plan is to make them Galactor members. Ryu is in the midst of those prisoners, but because he has taken away his bracelet, he cannot get into contact with Ken and the others. He decides to go along to the Galactor base. Learning of the incident, Nambu starts planning a trick operation to ambush Galactor. Ken, disguised as commander, has all the prisoners enter the God Phoenix, which is camouflaged as a Galactor transport airplane. He wants to draw some information regarding the location of the main Galactor base out of the Galactor leader who came to pick up the prisoners. Ken becomes a suspect and is consequently knocked unconscious. But the rest of the Science Ninja Team, with a tape containing pieces with Katse's voice, manages to continue the operation. The prisoners are cheated by a fake landscape built in the prison yard, and end up right back in the same prison again. Meeting his friends, Ryu thinks about the one man he met in the prison who dreams about going back home to his family.

The two countries of Bien and Ameria suffer from a long war. When the two countries finally make peace, their respective representatives standing for peace, Romina and Julia, get married as a symbol of peace. However, Galactor is planning to prevent the marriage of the two, to start the war again in both countries. The Science Ninja Team serves as bodyguard during the honeymoon trip. Joe thinks that the man he met in the airport, who supposedly has the same convictions as Romina, is suspicious. So he follows him, but loses sight of him near an old temple. Meanwhile, Romina and Julia are captured by Galactor robots. Ken and the others, still doing bodyguard duty, follow them, but lose sight of them. Searching the vicinities, they find the old temple. The Science Ninja Team sneak in and are attacked by a dove-shaped mecha. They fight hard, but a sun ray reflected off the compact Jun dropped, causes the dove mecha to self-destruct. When they intervene in the interior of the secret base, they discover Romina Julia, their whole bodies turned into cyborgs by Galactor. Ken offers them the possibility to escape, but they chose to die, becoming the reason for peace, rather than to live as puppets for Galactor's will. Embracing and kissing each other, the two changed cyborg bodies are wrapped in a lightning, smashing the Galactor plot to bits.

Galactor's Arkeo attacks the Moroi City. But Nambu judges that the Science Ninja Team is no match for the mecha's shock wave, therefore they don't receive orders to move out. Even when an announcement sent by Galactor arrives, the Science Ninja Team only gets an order to stand by. The Team ignores Nambu trying to stop them and gets mobilized. But they end up in a dangerous situation when they're hit by the mecha's shockwave. They are saved by Red Impulse. Ken yells at the angry Nambu that it's fine with him if the bracelets are given to the Red Impulse squad. The Red Impulse commander asks Nambu whether it would be possible to hand Ken and the others over to him. In the Red Impulse base, located in the South Sea, they start special training. Ken and the Red Impulse commander keep repeating the exercise of quickly pulling up with their planes. The other four watch Ken with sympathy. He is very happy, feeling like being with his father, even if he keeps protesting. For those four, the other Red Impulse members wait with a special training as well. In the middle of the training, Ken sees the waves caused by a pebble thrown into the water by Ryu and suddenly understands the aim of this training - Namely to invade the center of the shock wave. Again, an announcement of the next attack by Arkeo is received and the God Phoenix departs with the Red Impulse squad. By breaking through the shock wave and throwing bombs at the mech itself, they manage to make it explode. Ken, accompanying Red Impulse, does not know that this Red Impulse commander is his much sought-after father.

A secret mining factory of the ISO is attacked and the island on which the factory is located is besieged by Galactor. In the mine, an ore containing more energy than uranium is being mined. If this ore were to fall into Galactor's hands, the consequences would be catastrophic. Opposing the ISO which demands the protection of the ore, Nambu insists that saving the people has priority. The Science Ninja Team and a group of transport ships head towards the seal island where the factory is located. The island is hidden all year in a fog, and also Galactor is just standing there without being able to intervene. One group sneaks in, ducking under a Galactor attack, and gets near the island. They send G-4 to the island and he decides to get the workers out of there to the ships. He is able to hide them in a group of seals that had been surprised by a Galactor attack and are seeking shelter in the sea. The plan succeeds and the workers are saved, but the ore is stolen by Galactor's mecha. Also the fact that the workers could escape gets to be known. The transport ships are attacked and the workers taken as hostages. Katse threatens to kill the workers if the Science Ninja Team doesn't show itself. The Science Ninja Team appears in the dome atop the God Phoenix, but the moment the guns aim at them, the baby seal Jinpei took with him jumps into the sea. The Galactor members are distracted for a short moment by that noise and the Science Ninja Team seizes the opportunity to launch a counter-offensive. They succeed in reclaiming the ore from the mecha.

Ken is maintaining his beloved plane at the airport when a man with a gun forces him to fly a plane. Since Ken's plane has only a single seat, the man makes him fly another plane made for two people. During the flight, Ken seizes an opportunity and tries to take away the man's gun. However, the man fires a bullet which hits a wire in the fin tails of the Cessna, making it impossible to control the plane. The man, using the only parachute on board, escapes, saying that he will go to sell information to the ISO. Ken makes a forced landing, but because of that shock the radio device in the bracelet ceases to function. Ken sees a Galactor Mecha and follows the man who heads towards a valley. There is an abandoned Galactor mine there. Ken and the man are captured and hung up in an old well. The man has betrayed Galactor for money and has hidden a tape in the well which contains an overheard discussion between Katse and the Prime Minister of a certain country. Ken transmutes and rescues the man, defeating all the Galactor members in the building. But in an explosion occuring at that time, the man, who has seen Ken's true face and has followed him, is badly hurt. The Galactor commander, who got out alive, is about to attack them with a mecha. The man entrusts the tape to Ken, along with a message to his mother living in Hontwall, then he throws himself and the Galactor commander towards the bottom of the valley. What remains is the tape, which was smashed by the commander, and one name. "Kelly, Arthur Kelly is my name".

In order to finish an ultracomputer, Director Anderson himself is hand-carrying the core of this computer in his private jet to the research institute in the Jetol plateau. Galactor anticipates this, and starts to move in order to steal the component before it reaches the heavily fortified research institute. The Science Ninja Team, in the God Phoenix, takes over the guard duty for the director's private jet. But the disguised Katse has already taken the place of a stewardess. Katse eliminates the pilot and has the plane flown to the base guided by radio waves. Director Anderson notices the disaster and transmits a morse code signal with the radio attached to the seat. Ken and the others receive the signal and immediately follow the director's machine with the intention of getting it back. But they end up being led to the Galactor base. Just before arriving to the base, the director escapes using the ejector seat. But the core of the computer falls into the base. The Science Ninja Team and the Galactor members start a fight in a room, but through better teamwork, the Science Ninja Team gets the component back. Having gotten back the minister and the component, they blow up the Galactor base with a rocket and head afterwards towards the research institute in the God Phoenix.

Galactor plans to use the Shutterkiller to copy data from ISO institutions and to then destroy those institutions. The ISO institutions are attacked one after the other. The Science Ninja Team guards the institution which is most likely to be attacked next and, shortly pretending to have been defeated, follows the mecha in the G-4. Jinpei finds the Galactor base in the middle of the desert and goes on digging into the earth with his G-4. In addition, the other four team members follow him and sneak in. But when they enter the base, the G-4 machine is left unmanned. They start looking for Jinpei, and find a factory which restores the copied ISO data. Splitting up, they continue with destroying the factory and looking for Jinpei. Meanwhile, Jinpei has been taken along by a spaceship which is supposed to transmit rays from the mecha. Jinpei is saved and the factory destroyed, but Katse gets in the mecha and escapes. Attaching a wire to the mecha, Ken and the others follow him. Katse wants to shoot at them with the mecha's electronic laser flash. Ken notices this and throws his boomerang into the shutter part of the mecha. As a consequence, the mecha can't open the shutter and the laser hits its own interior. The mecha blows itself up. With a damaged hull, the Science Ninja Team returns to its base. But Katse will be back, showing his teeth.

The Science Ninja Team is accompanying Nambu, who came to the ISO headquarters for a conference. Jinpei discovers a car with the emblem of Galactor, hides in the car and goes to the Galactor base. But when he wants to get into contact with Ken, he is captured. Meanwhile, in Nambu's office, a message from Katse arrives saying that he will blow up ISO buildings unless the Science Ninja Team hands over some data regarding newly discovered uranium ore. Despite knowing that it's a trap, Nambu mobilizes the Science Ninja Team. Heading towards the location agreed upon, the God Phoenix is attacked by missiles from a mecha. Ken, using the many lobsters in the vicinity, causes the missiles to deviate from their course. Pretending to be done for, the case with the data is released into the sea, visible amidst some debris. The mecha collects the case and heads back to the base. In that base, the captured Jinpei escapes, sending a bird scramble. From that signal, the Science Ninja Team figures out the location of the base and breaks in, saving Jinpei. Realizing that the case is empty, Galactor presses the switch to blow up the ISO buildings, but through a trick of Jinpei, the Galactor base explodes. Jinpei is feigning to know nothing at all when the other four team members are very much astonished at the base blowing up.

In the country Inderia, droughts and heavy rainfalls occur every year. In cooperation with the ISO, a plan to build a dam in the hinterland to create lots of arable land is being made. But through mysterious events which are happening again and again around a shrine which will be inundated by the dam, the plan is progressing only very slowly. At long last, the Torakodon skeleton appears. The Science Ninja Team gets the order to investigate and sneaks into the country. Events like a landing transport plane exloding on the runway the God Phoenix was supposed to use, show the handwriting of Galactor. Jinpei and Ryu, staying in a cheap hotel, get involved in a murder case. Ken hears that the murder might have been connected to the fact that a golden coin has been found at the construction place. He thinks that the picture carved into the coin shows a secret underground passage way to the shrine and starts to investigate that shrine. While escaping, Ryu and Jinpei sneak into a Galactor base built in the cellar of the shrine and learn that the purpose of Torakodon is to have people stay away from the missile construction plans in that base. Ken and the other sneak in from the street and together they destroy the missiles. They blow up the control mechanism for Torakodon and defeat the Galactor members, afterwards they leave the rest to the local police and depart from the country. Then, just as Katse arrives in Inderia, the base explodes before his eyes.