Goofy-bunny Mr. Whiskers meets prissy-pooch Brandy Harrington within a cargo hold of a plane. When Whiskers mistakenly opens the hatch door, the pair is dropped into the Amazon Rainforest with no way home. Desperate and angry, Brandy makes a deal with the dictator lizard Gaspar: a way back to civilization in exchange for Mr. Whiskers as his dinner. In the end, she loses her way home, but truly gains a friendship with Lola Boa and Mr. Whiskers.

Brandy volunteers to watch a crocodile’s eggs for the day, but when Lola Boa and the Toucan Twins invite her to hang out, she leaves Whiskers in charge. It goes as well as expected with Whiskers losing the eggs and mixing them up with those of other animals. Now he and Brandy must retrieve the correct babies to avid Mama Croc swallowing them whole.

Spring is in the air as Whisker’s falls in love for the first time: with a giant lizard, Isabel (Jennifer Hale). She wants nothing to do with the smelly rabbit, but Coach Brandy is determined that Whiskers can woo her. Meanwhile, Brandy has her own issues in fighting off a persistent little lemur (Charlie Adler & Jeff Bennett).

While out star-gazing, the gang meets the cosmonaut monkey Boris (Greg Baldwin), having crash-landed into the jungle. Though his shuttle comes equipped with a rescue signal button, he refuses to push it and have the humans return him to space. While Brandy schemes to call for her own rescue, Mr. Whiskers is having fun playing spaceman and thwarting her.

Mr. Whiskers, being bullied by a cruel neighborhood monkey, must find the confidence to stand up for himself before it drives him away from Brandy. Meanwhile, Brandy is on a mission to increase her public image in the jungle. Instead, she learns the importance of standing by your friends, even the uncool ones.

Brandy is hosting a slumber party for girls only, kicking Whiskers out who forms one with Ed. Neither party is going too well until Whiskers begins a prank-war that quickly escalates into real trouble for everyone.

Brandy wants to try to introduce fashion to the jungle. The jungle denizens proclaim Mr. Whiskers is a fashion genius.

It's Brandy's birthday though she is unhappy because it's her first birthday away from her family. She believes that it's also Whiskers' birthday as well.

Brandy is preparing for the Harrington Ball, which is a formal dance that the Harringtons have every year, but with all the hard work she forgot to get herself a date! She has Whiskers, and teaches him some etiquette manners.

Brandy, disgusted with Gaspar’s dictatorship, riles the jungle dwellers to hold an election for king. She and Whiskers win the job, but quickly abuse the power just as bad as Gaspar, if not worse.

Brandy stumbles across a suitcase that they weren't aware of, she finds a portable video game and she gives it to Mr. Whiskers to get him to stop bothering her. In the end, he finally has to save Brandy from falling off a cliff.

Mr. Whiskers helps a jaguar named Lorenzo (Bobby Slayton), but when his driving Brandy and Mr. Whiskers at the hook they try to find a way to get Lorenzo out of their lives. Lorenzo invites his family, which Brandy puts a stop to. In the end, Whiskers helps another huge creature with the same problem.

Brandy and Whiskers see a relationship therapist, Whiskers takes an exercise too far and pretends that he's Brandy, and vice versa. Everybody thinks this, except Brandy. In the end, Whiskers is back to his old self.

An Ocelot named Artaro catches Brandy's fancy, in which they fall in love and plan to go out on a date. Mr. Whiskers feels that Artaro is actually evil, and he tries to convince Brandy to not go out with him but it turns out that Mr. Whiskers is actually right.

When Mr. Whiskers finds out about luck, he believes his feet will provide him with the luck he needs to remain safe and get anything he wants, much to Brandy’s dismay.

When Brandy introduces money into the jungle, she discovers its hard to live a life of luxury when you have to earn your finances. In the end, Whiskers pulls out what appears to be a huge emerald. Brandy exclaims that she is rich.

When Brandy tells Mr. Whiskers to read something because he has too much time on his hands, she inadvertently leaves her Diary out in the open, in which Mr. Whiskers reads because of her suggestion. After a while he starts to read everyone else's diaries, too. In the end, Whiskers gets tied upside down as punishment while Brandy befriends the spider who has about to devour him.

Brandy is holding a food drive for the less fortunate, in which Mr. Whiskers wants to help out. However, when Mr. Whiskers accidentally ruins the food drive, Brandy needs to find a way to make it work out anyway. So Mr. Whiskers becomes a superhero after reading a comic, but when everyone says that he's a menace, he decides to become a supervillain.

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When Brandy and Mr. Whiskers try to eat the tastiest fruit in the jungle, Brandy finds out that the fruit tastes like dirty socks. As Brandy marches off in frustration, she kicks down an ant hill, leaving it exposed to the ant eaters who attack the hill on a regular basis. The Sargent Ant goes after Brandy to get her and Mr. Whiskers to defend the ant hill until the mound can be fixed, but will Brandy agree to join the ant army, and will she even be capable of defending the hill from the ant eaters, or not?

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While enjoying themselves at the river, Mr. Whiskers inadvertently crashes into Ed after Ed crashes into a log, which causes Mr. Whiskers to fly into a Mayan temple. Inside, they discover an ancient monkey's paw that grants wishes, in which Brandy decides to use to get back home; though the ancient artifact is much different than they anticipated.

Brandy and Mr. Whiskers stumble across an old tree, in which Brandy learns that the tree is of a rare kind that is capable of building a vessel capable of getting her back to Florida. Brandy manages to convince the animals who live in the tree to move into her house so she can cut it down, but Mr. Whiskers is refusing to leave the tree because he feels it shouldn't be cut down. Will Brandy be able to get the tree cut down and get back to Florida or will Mr. Whiskers prevent her from even touching it?

Brandy prepares for a big coco ball match against Gaspar Le Gecko's team, which is the best in the jungle. However, despite her attempts to train the team, Ed the Otter keeps messing up and causes the team trouble. Brandy knows that Ed will not do a good job during the big coco ball match and she needs Mr. Whiskers to cut him from the team, but will Mr. Whiskers be able to cut one of his best friends from the team or not?

Brandy realizes that it's getting very close to Christmas, so in an attempt to try to get back home, she spreads the word of Christmas to the Amazon and they all prepare for his arrival, as Brandy thinks Santa would have no choice but to arrive if people are looking forward to him coming. However, when Santa does arrive, she realizes that he doesn't want to take her home, as she's been too naughty to gain such a reward; Brandy, in anger, tosses a lump of coal he gave her at him, which causes him to crash his sleigh into the ground. Now, Brandy must take on the mantle of Santa Claus and work with her friends to deliver presents to all the world's girls and boys, though will she shirk her responsibilities once she gets home to Florida like she plans?

With Gaspar Le Gecko's oncoming beauty pageant coming up, and the grand prize being a vacation to Palm Beach, Brandy decides to enter the contest so she can get home. But unfortunately for her, she stumbles upon documents that prove she was adopted into her lineage. Will she be capable of overcoming this knowledge despite the fact that she isn't a real Harrington, or will the fact that she's a mixed breed crush her spirits for good?

After Mr. Whiskers dirties up the house Brandy just cleaned, she decides that she has had enough of him and she kicks him out. While Mr. Whiskers tries to find a new family to live with, Brandy looks for a new roommate who will share her interests, but will they both be happy with their new lifestyles?

Mr. Whiskers accidentally destroys Brandy's favorite scarf when he barrows it in order to entice some boars. With Ed's help, Mr. Whiskers formulates a plan to shed his own hair and make Brandy a new scarf, but will Mr. Whiskers be capable of doing his plan, all the while keeping Brandy from finding out the truth?

When many of the jungle denizens have items go missing, all the evidence points towards Brandy. Brandy is arrested and sent to jail, though Mr. Whiskers vows to help find out who the real criminal is. But will Mr. Whiskers actually be able to prove Brandy's innocence, or is she even innocent at all?

When Brandy becomes friends with another dog, Tiffany Turlington, Mr. Whiskers begins to feel left our and jealous. He attempts to find a relative of his to get back at Brandy while Brandy enjoys her time with Tiffany, but will his attempts work?

When Mr. Whiskers discovers that Easter is near, he becomes ecstatic and begins to celebrate. However, when he keeps Brandy up all night, she tells him that the Easter Bunny isn't real and it breaks his spirit causing Brandy to feel bad about him, but will she be able to find a way to make it up to him?

Brandy and Mr. Whiskers have a try at the jungle's biggest sport, Leaf Boarding. Brandy feels she will be the best with her past experience in snowboarding, while Whiskers is afraid to even try the sport due to his overwhelming fear of plants that occurred during his youth. However, Brandy does horrible at the sport while Mr. Whiskers may just be the best Leaf Boarder in the Amazon. With the upcoming Leaf Boarding championship coming up, will Brandy manage to improve her skills or will she embarrass herself completely?

After Mr. Whiskers attempts to install a skylight into the house, nearly destroying it all in the process, Brandy insults him claiming that he doesn't think things out. When Mr. Whiskers consults Ed for advice, he goes to the Forbidden Swamp, obtaining himself a second head, one that is incredibly smart, polite and charming. While his new head is quite popular with the other jungle denizens, he himself begins to doubt that getting a second head was wise.

Whiskers has been depressed recently and while they cannot find the cause of his depression, Brandy has an idea to cure his depression, an all out shopping spree! However, Whiskers becomes addicted to shopping and things get even worse then Gaspar gives Mr. Whiskers a Gaspar Card. Brandy, however, knows that credit cards are bad business, but will she be able to stop Mr. Whiskers?

After Brandy and Mr. Whiskers get into a fight over Mr. Whiskers junk cluttering up the house, Brandy shoves Mr. Whiskers old meat in the back of his jump suit. However, when the meat attracts predators and Mr. Whiskers jumps off a cliff to save his life, he finds himself trapped. Brandy, with Lola's advice, goes and rescues him. Mr. Whiskers makes himself Brandy's personal servant until he can pay her back, but will Brandy really enjoy having Mr. Whiskers as her servant or will he end up driving her crazy first?

Brandy and Mr. Whiskers find a baby Tapir after their picnic gets ruined. Brandy decides to take care of the baby until they can find its parents and she leaves the baby in Mr. Whiskers' care until she can find out more about the child. However, when the baby begins to look at Mr. Whiskers for a role model, Brandy is upset because Mr. Whiskers doesn't grasp the concept and begins to teach the Tapir some poor behavioral choices.

Mr. Whiskers is upset because he doesn't have many friends and is highly unpopular. However, when Mr. Whiskers inadvertently swallows a piece of a meteorite and turns into a living radio, he discovers that he may have just of found a method to become popular, though will he find popularity to be all it's supposed to be?

Brandy and Mr. Whiskers discover a camcorder set while Brandy is trying to send out S.O.S. messages in a bottle. Brandy decides to make a quick movie and send it instead to increase her chances, but Mr. Whiskers gives her the idea to make a blockbuster as a rescue tape. Brandy buys into the idea instantly and Mr. Whiskers gathers a film crew from the jungle denizens, but will the movie production go as planned?

Mr. Whiskers has been depressed because he has been unlucky recently so Brandy decides to give him a simple task to boost his self-confidence, in which she requests he go pick a wild onion. Mr. Whiskers does so, but upon picking up the onion he is proclaimed the Great Grooter by a pack of wild rodents which increase Mr. Whiskers' confidence, though is it in the manner that Brandy wished for?

Brandy is attempting to teach Lola Boa how to give a pedicure while Mr. Whiskers is attempting to become a one bunny orchestra. However, their two goals soon collide and they get into an argument. Lola Boa threatens Brandy and Mr. Whiskers into going to see a relations counselor, who suggests that they try role-playing as one another to express their true thoughts. However, when Mr. Whiskers continues to role-play when the two return to their home, things take an unexpected turn as all of Brandy's friends begin to believe that Mr. Whiskers is the real Brandy.

When Mr. Whiskers falls out of the tree for yet another time, Brandy insults him, saying that he never uses his brain. However, Mr. Whiskers' brain agrees with her, so he decides to leave his brain and head off to live his own life. Mr. Whiskers begins to become depressed as he feels lonely without his brain inside of his head, so Brandy decides to head off to find Mr. Whiskers' brain in order to return it to the rightful place where it belongs, though how will she manage to convince his brain to go back to the place he hates?