Otis and Pip pretend to be superheroes Cowman and Ratboy, but the other animals are not fond of their antics. Fortunately, when Otis and Pip rescue the Pizza Guys from falling off a cliff, the animals decide to join them as superheroes.

After Otis saves Duke's life by pushing him away from a falling amplifier, Duke begins getting loyal to Otis and becomes devoted to helping Otis doing everything, but Otis soon becomes annoyed when Duke goes overboard.

When Pig's truffle pies become a huge hit in the barnyard, the animals decide to use Pig's pies to sell them to the humans to make money, but Pig quits when the animals begin to get greedy with trying to make money, especially when a celebrity comes to buy the pie recipe from them.

A space test monkey named Bingo crash-lands in the barnyard. The animals decide to let him stay in the barnyard, but Bingo is unsatisfied with the fact that Otis is the leader, so he tries to get rid of Otis so he can become leader.

Otis' pranks and Abby's driving lesson has Mrs. Beady sent to a mental institution. Feeling guilty, the animals try to rescue her, much to their dismay: Mrs. Beady's doctor wants to put her on a brain transplant when he thinks Mrs. Beady has "crazy brain" because she sees the animals out the window.

The animals are unable to have Saturday night parties because of the farmer constantly weeping about his lost wife. Otis finds him the perfect girlfriend to make him feel better, but they then realize that she is trying to get rid of the farm animals by kicking them out of the barn and take it over (forcing the animals to stay in the hen house which explodes because of the max capacity of the animals in there). So they dress Pig as rich man to lure the woman away from the barnyard, but Pig wouldn't lie and he confessed to her, which makes the woman leave the farmer. In the end, the animals get to have their Saturday night parties, Pig is heartbroken (which he stops after a few minutes), and the farmer went on a cruise with some ladies.

When Otis gets a hypnosis kit, he accidentally hypnotizes himself so that he tries to destroy the farmer whenever he hears the sound of a bell. Now, the other animals must try to protect the farmer while trying to cure Otis at the same time. But every time Abby tries to stop Otis from hurting the farmer, he thinks she is hurting him.

With Peck nowhere to be seen and Freddy seen lying on Peck's feathers, the animals conclude that Freddy ate Peck and plan to ban Freddy from the barnyard (Duke locks Freddy in a 'scented' pet carrier to attract the pet store truck driver so Freddy would be adopted). Otis is determined to prove that Freddy is innocent, however.

Otis is embarrassed when Abby repeatedly beats him in the Barnyard Olympics, so he tries to find Abby's weaknesses and use them to his advantage.

To get revenge at Bessy's insults, Otis tries to humiliate and embarrass Bessy, but at every attempt, the prank backfires. Bessy subsequently gives Otis a real (and humiliating) prank that ends up him and Pip covered in honey and seeds.

After Otis accidentally destroys the barn's safety film, he must make a new one, which he puts a lot of action and suspense in. When the other actors quit because of the dangerous stunts, Otis must make it on his own, and accidentally rises the barn into a tornado. In the end, Bessy makes the safety film all about Otis' unsafe antics.

Otis is excited because favorite country music star – Stumpity Joe – is coming to town. However, when trying to speed up crop collecting for the farmer to leave, he accidentally injures the farmer. Now, the animals must do all of the farming, or else the farm can go bankrupt. But several things had gone wrong because the animals aren't accurate farmers themselves. Otis milks himself wrinkly with the milk machine, Bessy and Abby refuse to use the milk machine on themselves, Pig eats all of the corn they picked (making him very fat), and Freddy goofs with the energy drink for the hens by putting dynamite in it, which he claims it is pepper, making the eggs the hens lay explode on contact.

A hedgehog named Don Bling convinces Otis to fight in a wrestling match but it turns out that all of the matches are fixed so then Otis' opponents all lose intentionally. Now, Abby, Pig and Pip must try to stop the hedgehog before Otis fights someone who is really trying.

When Duke tries crazy methods for the sheep to be safe during bear season, they escape and now Otis and Duke must go on a cross country trip to get them before they escape to New Zealand. Meanwhile, Abby and Bessy dress Pig, Freddy, and Peck as sheep. But it backfired when the farmer thought Pig had the "nervous woolies" when Pig accidentally said "Beeeee" and "Boooo" instead of "Baaaa".

After Mrs. Beady videotapes Otis and the gang walking and talking, she calls a news station to prove she isn't crazy with proof from the tape. The animals don't like it at all, though. Now, they try to interrupt the broadcast to not let any person see their everyday anthropomorphic behavior (and fulfill their dreams of becoming famous television stars). But it backfired, when the cameraman got a call from the network saying they're not on the air, leading the news station to change the animals' tv show back to the broadcast. So now the animals must now steal the tape to keep anyone from seeing their antics.

When the veterinarian stops by, she mentions that her van, the "Big Steer", won't last a week. However, Otis mistakenly thinks the veterinarian was referring to him and begins to think that he only has a week to live. To relieve himself, Otis tries to do everything he has ever dreamed of. When he returns, the animals are happy that he was gone so he abandons them. When he tried to do a jump over a canyon, he fell to the bottom and got injured. After that, the animals apologize to him for kicking him out of the barnyard.

This week's Moose Appreciation Week, so Otis disguises himself as a moose so he can get positive attention from humans, but his plan goes awry because the week is over and now the Moose HUNTING SEASON starts today and now Snotty Boy and his friends are trying to hunt him down, and his antlers are stuck to his head. So the animals rigged a robotic moose to scare Snotty Boy away from Otis. But Snotty Boy accidentally goes out on a busy road. So Otis has to save him from being hit by a car. Because of his heroism, the county now bans Moose Hunting Season and makes it Moose Appreciation Week all year long.

Upon realizing how lame his friends are: Freddy and Peck dressing him up as a bunny instead of a monster to scare away crows, Abby inviting him to bingo, and his friends habits at bingo (Pip's loud keyboard typing, Duke's squeaking his toy, Abby's slurping on a drink, and Pig digging in his ear), Otis ditches them and goes out for a night on the town, pulling pranks with the Jersey Cows. Otis, unfortunately, ends up getting arrested. So now his friends have to come get him out and stop the police officer from taking him away again.

Otis' favorite circus is coming to town, but the gang accidentally injures the main lead. Feeling guilty, Otis offers to take over and along with his friends, but Abby is too afraid to do her part because of an incident that happened long ago: She had dropped her partner when trying to catch him. Abby refuses to do the part because of being afraid to drop Otis. But without Abby, the show ends up being a disaster

After the gang notices a distinctive birthmark on Pig's backside, Pig starts to believe that he is related to the royal Pampered Pigs. After training Pig, he becomes snobbish to his fellow companions.

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.

Freddy tries to hide his non-carnivore ways from his parents, who are invited to a birthday party at the farm, and Freddy tries to make sure they don't eat anybody, including Peck, while keeping it a secret to his friends.

After Snotty Boy returns to torment the animals, Otis accidentally falls on him and becomes unconscious. Luckily, he's got a pulse and they decide to take him back to the Beady's, but Abby says that Mrs. Beady will blame them. Otis sends a disguised Pig over to the Beadys' as Snotty Boy so they don't get suspicious. But Pig enjoys being Snotty Boy so much that he decides to stay as him forever. Meanwhile, Snotty Boy gets amnesia and the animals realize that the only way to get Pig back is to turn Snotty Boy back to his old mean, obnoxious jerky self so Mrs. Beady will recognize him and because Snotty Boy is annoying them with his newly found kindness and sweetness.

Otis' negligence causes Pip to get captured by Snotty Boy, who plans on feeding him to his new pet snake (who talks exactly like him).

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.