The animals become pop stars when Pip broadcasts one of their sessions, but soon their egos begin getting out of control and begins to put a damper on their friendship, which eventually causes a heartbroken Peck to quit.

When it's discovered that Pig has a beautiful singing voice, Otis and the gang enter Pig in a singing competition to win the farmer a golden tractor. When Mrs. Beady loses, she is out to prove that Pig is a talking barnyard animal. Meanwhile, Pig's over-practicing causes him to lose his voice. So Otis tries to use lip synching but he doesn't know the lyrics in the song, so Pig is booed for singing terrible lyrics. In the end, Pig did win a prize (a tiny tote bag), but they couldn't keep the tractor they stole because it was illegal to steal a grand prize without approval of winning.

Peck takes a fake potion to get enough courage to speak to his crush, Hannah, but he ends up being so confident that he challenges Root, a rooster much bigger than him, to a duel.

Otis must take over teaching (in the stern of Bessy) after accidentally injuring Peck, the children's teacher. When he realizes that the kids learn boring things, he teaches the kids how to pull pranks. However, the kids develop an ultimate prank, which sends the barnyard silo to mid air, just when all of the animals are in there to hide from Duke, who appointed himself as new leader.

Otis and his friends dress up as girls because the bowling alley is open, but only girls get to go free. Their plan backfires when Snotty Boy and his friends try to take them out on a date. They are forced to agree when they realize that Abby and Bessy have put glue on their women's clothes so that they can't take them off and they can't throw them off because Pip removed the stink bomb from the purse to make room for himself. After one night, the other animals couldn't take it anymore, but Otis still continues to go out as a girl so he can get free things from Snotty Boy. Everything goes well until Otis realizes that Snotty Boy has engaged to him.

Otis uses Crazy Louie – a loopy groundskeeper at a high-end golf course and apparently his friend – to let him and the animals through the back gate and play a round. When Pig throws a club and accidentally hits Louie in the appendix, though, a guilt-ridden Otis decides to win the big golf tournament to get a new appendix.

When news anchor Hilly Burford is crushed covering a giant cheese curd that Otis made, the animals fill in for him on the news. They turn out to be a huge hit and replace Hilly, but Otis doesn't want them to replace him so they try to convince Hilly to get back to his job.

The animals feel bad for the Farmer after seeing that everyone forgot his birthday, so they decide to throw him a party and tell him it's a dream, but the Farmer gets carried away. He does this by stealing a motorcycle from a gang of bikers and then believes that the motorcycle can fly so he takes the veterinarian with him. But he forgot that it doesn't and he and the veterinarian ends up falling to the ground below. So Otis hurries to save them before they fall to their death.

When Otis injures himself, Pip temporarily takes over as the barn leader, and when he recovers, realizes that the others think Pip is a much better leader than Otis was. Insulted, Otis decides to leave the barnyard and be a leader where he's needed – with a den of beavers.

When Pig cooks up what appears to be permanent glue, the animals try to sell the glue to make money. They soon realize that the glue explodes two hours after it is applied and must find a way to get rid of it safely. When they found all the glue from all the buyers, they realized they sold 500 pounds of glue to city hall so that the town can use it to patch the town's cracked manure tank. So the animals race to dispose the manure tank before it floods the town with manure.

Duke wants a playmate, but no other animal wants to play with him, so the animals convince the farmer to get Duke a playmate. Unfortunately for Duke, the farmer brings Duke's arch-rival Baxter back to the farm, and Baxter causes trouble with the farmer while blaming everything on Duke, getting Duke in trouble and being put in the barn with the other animals. They try to stop Baxter but the farmer scolds them for hurting him. So they dress Otis as a bear so that Baxter pushes the farmer to it and get Baxter in trouble. The plan works but Duke accidentally attacks a real bear instead because Otis was late on cue.

The animals claim the farm as a protected habitat to prevent a wreck crew from tearing it down and disguise Freddy as a spotted three-toed ferret. They then realize that this species is real, and a real female spotted ferret is shipped to the barnyard and Freddy falls in love with her. Sadly, the animals realize that female spotted ferrets eat male spotted ferrets when they marry, so the gang must get rid of her. Freddy is then heartbroken after his friends stop the wedding because he lost his one true love.

Pig has been hanging out with his imaginary friend, Mr. Wiggleplix, for weeks and it drives the other animals crazy. Then one day, Pig claims that Otis killed Mr. Wiggleplix so Otis has to dress up as Mr. Wiggleplix for Pig to feel better. Things take a turn for the worst when Otis says he is leaving for a magical land but Pig believes it and wants to go with him. All of the sudden, the real Mr. Wiggleplix comes alive and stops Otis from impersonating him.

After Otis accidentally breaks up Peck's body with a hammer, he rebuilds Peck by adding robot parts to him so he can be a big help around the barnyard, but things go awry when Peck's circuits get overloaded after Otis puts pizza inside him and he goes out of control.

The farmer is in love with a woman named Branco Betsy who's a rodeo host and is interested in bull riders, so Otis pretends to be the farmer's bull so Branco Betsy would be impressed. At the rodeo, however, Otis meets Psycho, a much bigger bull, who injures him, so now the farmer has to ride Psycho, the big (and dangerous) bull.

Mrs. Beady has no choice but to move with the barnyard animals after being kicked out of her house and being mistreated by Mr. Beady's mother, Mother Beady.

When a beautiful she-donkey named Prunella takes an interest in Pip, Bessy suspects ulterior motives and follows them on their dates, causing the other animals to accuse her of being jealous.

A group of Canadian Crows want to steal the corn from the barnyard, but after repeated failed attempts, they decide to give the animals a fake treasure map to distract them from guarding the corn.

While trying to escape Snotty Boy, the animals run over Snotty's clown father. His dad survived, but has lost a lot of hilarity and Pig takes him into surgery. Otis disguises himself as Snotty's father to distract him while he recovers and becomes a cool dad to Snotty Boy. Only Snotty comes to love and admire Otis in a way he never did for his lame clown father. Otis has to think fast before he ruins this miserable family.

Otis and his friends become cops after another cop gets injured, and they try to solve a crime that is about stealing in a donut store. They find the suspects are Mrs. Beady, Snotty Boy and the Farmer. They try to interrogate them, but they're all innocent. They then learn that Pig is the real thief because he wore a burglar costume every time he goes to get donuts for his friends.

The animals call Dr. Filly to settle a recent persistent argument between Freddy and Peck, but instead of making things better, Dr. Filly seems to make it worse when other animals begin disliking each other. They were almost going to leave (except Bessy) until Otis reveals that "Dr. Filly" is an imposter donkey named Chip who likes to impersonate Dr. Filly.