Pip's mousehole is destroyed by Otis accidentally. He moves in with the others, but they're all unused to each other's habits. After hearing a misunderstanding that is impossible to share a home with Pip, he runs away and finds a bee hive. Otis and his friends must search for him and return him to the barnyard.

Otis discovers that he has the same bell as Bessy's long lost child, so Bessy believes that Otis is her child, so she starts treating him like a child and humiliates him and refuses to let him goof around and do pranks on Mrs. Beady.

Abby discovers Otis' secret club, but the animals don't want a female member there so they pretend the club is very boring so Abby would leave. Soon, though, Abby discovers that Otis is faking, so she creates a club herself. Now everybody wants to join her club and Otis is left alone.

When the gang gets caught by Snotty Boy in a game of "Dungeons and Barn Animals", they make Snotty believe he is in the mythical land of Barnia, and now the animals must force him out before he takes over the barn.

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.

A bunny's ghostly spirit possesses Pig after Otis builds a fun shack over a pet burial ground, and wants to take over the barnyard and reclaim the world.

Otis becomes afraid when he receives a letter from his childhood bully, Krauser Krebs, saying that he's coming to visit the barnyard, so his friends try to help him defend his fear of the bully.

Otis loses the saloon to Chubs Malone, head of the gopher underground, in a game of Fizzbin. Now, the gophers dominate the barn at night.

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.

Bigfoot is sighted in the woods, and Otis decides to go hunting for him, but Abby finds him and brings him to the barnyard for his protection. Mrs. Beady, however, is out to capture Bigfoot and prove she is not crazy.

Otis becomes the county's new crop dusting ace. An accident causes him to quit, however, and at the wrong moment: a large swarm of locusts is about to destroy the crops.

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.

When Mrs. Beady tries to run for mayor, Otis decides to run for mayor against her to avoid Mrs. Beady from exposing them as talking animals. Their competition goes horribly out of control, however.

When Freddy gets depressed over his lack of talent, Otis and the gang decide to make him take up ventriloquism. The dummy that they make, Mr. Jinx, comes alive, however, and tries to kill them. It turns out that a colony of termites has possessed Mr. Jinx to get revenge on them for using their tree to create Mr. Jinx.

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.

When Otis as Cowman is assigned the task of guarding the Jurassic Corn Kernel at the county fair, Mertin Fargleman (voiced by Tom Kenny) wants to steal it to win the Gardening Award posing as Professor Twineyvines. When the town is impressed with Twineyvines and unimpressed with Cowman trying to save the Kernel from him, Twineyvines becomes the new protector. Immediately, Otis takes the kernel to protect it and is branded a thief and then chased by a mob. He then decides to stop Twineyvines when Abby finds Otis and Pip headed for Peru and says that Peck, Pig and Freddy have been kidnapped by Mrs. Beady, who they do not know is in line with Twineyvines. Now, Otis, Pip, Abby, Pig, Freddy and Peck must unite to defeat Fargleman, clear Cowman's name, and save the Jurassic Corn Kernel (mutated into a giant monster) from destroying the fair (even though the fair was already destroyed).

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Pig returns to his birthplace to be married, but after Otis realizes that Pig's bride, Brunhilda, is cruel and bratty, he tries to stop the wedding by beating Pig in a contest.

Otis' new Kobe cow neighbors begin to think that he's the reincarnation of the legendary Sun Cow when they discover Otis has a fifth udder (which was actually a bee sting). Otis is glad he has that status until he realizes that the cow neighbours actually serve "Sun Cows" at a steak restaurant and they're planning to do the same to Otis.

While Duke is at the vet after being sprayed by Pig’s skunk, a mischievous mutt named Baxter sneaks out and goes to the barnyard while disguised to look like Duke for what his life is.

Under Abby's request, Otis takes in a clam that she rescued from a nearby café. However, the clam is a rude and demanding house guest. It hogs the shower, Pig hanged up on a radio contest that Otis was calling to for temperatures in the barn, it takes over the barn at bedtime and, to make matters worse, it reproduces many party-going clams. Otis believes that Abby will get in trouble with the farmer once he finds out she is the one who brought all the clams into the farm and decides to relax while the other animals are stuck with the millions of clams. Soon they do not want to leave and instead bile Otis when he tells them to get out. Now, the animals must figure out how to calm them down.

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.

After the animals break the farmer's classic video game system, they need to make some quick cash to replace it. Seeing an ad to babysit, they dress up as British nannies and show up at the address on the ad. Only when Mrs. Beady answers the door do they realize they're babysitting Snotty Boy, but Snotty Boy wreaks havoc on them and the animals have to get the little terror fed, bathed and into bed before the Beadys get home and earn the money for babysitting.

The animals get arrested when they are mistakened by the police for bandits disguised in animal costumes. Chained together, they try to escape so that they can use a computer to find the real thieves. But when they do catch the real thieves, the police says due to budget cuts, they aren't any keys to free them from their chain, so now they're stuck chained together

Otis convinces his college buddies Donner and Blitzen to stop by the barnyard on Christmas Eve. During the visit, Otis accidentally gives Santa a cup belonging to Freddy, who is sick. When Santa comes down with Ferret Fever and can't finish his rounds in the county, which turns out to be his last stop on his Christmas Eve rounds, then Otis and the animals vow to make toys and deliver them by midnight to save Christmas. Meanwhile, Snotty Boy, not knowing he’s on the naughty list, really wants a Red Rider BB Taser that Santa doesn't bring him every year. So he sets a trap for Santa to make sure he brought his present.