It's Otis' birthday so he makes a prank call for the farmer to leave the barnyard for a day so they can have a party. But his plan backfires when the farmer hires Snotty Boy to babysit the farm animals.
When the farmer is seen with what appears to be a barbecue grill, they become afraid that the farmer plans to eat the animals, so they escape the farm on a hot air balloon.
Otis and Pip think there is too much crime at the barnyard, so they become superheroes: Otis as Cowman and Pip as Ratboy. After the two save the Pizza Twins from driving off a cliff, they try to get the rest of the animals to become "The Justice Brood."
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 soon Otis becomes annoyed when Duke goes overboard.
When Pig's truffle pies become a big hit with humans, Otis convinces the gang to transform the barnyard into a restaurant so people can get another helping of Pig's delicious pies. But when the fortune gets in the way of their lives, Pig quits, just before a wealthy millionaire (voiced by Maurice LaMarche) offers to buy the recipe for a million-bajillion dollars.
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.
The animals are unable to have Saturday night parties because of the farmer constantly weeping about his lost wife. So Otis finds him the perfect girlfriend. But then they realize that she is trying to get rid of the farm animals.
Otis gets a hypnosis kit and accidentally hypnotizes himself so that he tries to destroy the farmer whenever he hears the sound of a bell. So the other animals must try to protect the farmer while trying to cure Otis at the same time.
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). But Otis is determined to prove that Freddy is innocent.
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 every time the prank backfires. So Bessy gives Otis a real (and humiliating) prank.
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 it. When the other actors quit because of the dangerous stunts, Otis and Pip must make it on his own, and accidentally rises the barn into a tornado.
Otis is excited because favorite country music star – Stumpity Joe – is coming to town. But 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 would go bankrupt.
A hedgehog named Don Bling convinces Otis to fight in a wrestling match but it turns out that all the matches are fixed, and Otis' opponents all lost on purpose. 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.
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. But the animals don't like it one bit. 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).
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.
Upon realizing how boring his friends' bingo club is, Otis ditches them and goes out for a night on the town, pulling pranks with the Jersey Cows. But Otis ends up getting arrested.
It's Moose Appreciation Week, so Otis disguises himself as a moose so he can get positive attention from humans. But it goes awry, when Snotty Boy and his friends try to hunt him down, and his antlers are stuck to his head.
Otis' favorite circus is coming to town, but he 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.
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.
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.
When Snotty Boy returns to torment the animals, Otis falls on him, causing him to have amnesia and become nice. Snotty's aunt Mrs. Beady doesn't recognize him and denies that he is indeed Snotty Boy so Pig must go in disguise as Snotty while the animals find a way to get the old Snotty back.
Otis' negligence causes Pip to get captured by Snotty Boy, who plans on feeding him to his new pet snake (who talks just like him), so the other animals must find a way to rescue 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 the others that it's 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 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 him to goof around.
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. But when Abby discovers that Otis is faking, she creates a club herself and now everybody wants to join her club and Otis is left alone.
Snotty Boy believes he is in the mythical land of Barnia while playing a game of "Dungeons and Barn Animals" with the rest of the gang.
Otis enters Pig in a singing contest, but Pig loses his voice before the finals after being pushed too hard during practice.
After Otis builds a fun shack in a pet cemetery, Pig becomes possessed by the ghost of a mean-spirited bunny.
When Otis receives a threatening letter from a bully from his childhood, the animals rally to assist him in confronting the hostility.
When Otis loses the saloon in a rigged game of Fizbin to Chubs Malone, he tries to win it back by cheating but gets caught.
After being encouraged by Otis, Peck takes a potion to bolster his confidence enough to speak to the hens, which results in his challenging one to a duel.
Otis is more than annoyed with Abby after she captures Bigfoot and harbors him at the farm.
When Cowman is assigned the task of guarding the Jurassic Corn Kernel at the county fair, Professor Mertin Fargleman (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, Cowman takes the kernel to protect it and is branded a thief and then chased by a mob. He then decides to stop Twineyvines when Cowgirl finds Cowman and Ratboy headed for Peru and says that Green Rooster, Mr. Hamtastic and Paranoid Man have been kidnapped by Mrs. Beady, who they do not know is in line with Twineyvines. Now, Cowman, Ratboy, Cowgirl, Mr. Hamtastic, Paranoid Man and Green Rooster 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).
Otis becomes a crop-dusting ace, but stops flying when he crashes. He later has to face his fears when a swarm of locusts head for the town.
After Otis injures Peck, (who is the kid animals' teacher) he takes over as schoolteacher. However, he decides to educate them about fun instead. But the kids go too far and lauch the animals into the sky with a silo.
Otis runs for mayor against Mrs. Beady to prevent her from creating anti-talking animal laws and they run a brutal campaign.
Otis and the gang make Peck a ventriloquist dummy to cheer him up about his lack-of-talent depression. However, the dummy starts trying to eliminate the gang, and they think Peck's doing it.
Otis and the boys dress up as human girls to crash a laser bowling alley grand opening, but things go wrong when Snotty boy asks Otis out.
Pig returns to his birthplace to be married, but after Otis realizes that Pig's bride 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, a mischievous mutt named Baxter sneaks out and goes to the barnyard while disguised to look like Duke. Later when the two dogs are together the animals can't tell them apart, despite them looking obviously different to the audience.
Otis takes in a clam that Abby rescued from a nearby café. However, the clam is a rude and demanding house guest and, to make matters worse, it reproduces many party going clams. And they don't want to leave.
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. But when Pig throws a club and accidentally hits Louie in the appendix, a guilt-ridden Otis decides to win the big golf tournament to get a new appendix.
After Otis breaks the farmer's classic video game system, the animals 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 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.
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.
Otis is bored of Abby's book club so he releases Wild Mike from a cage so they can have a dance party. But Wild Mike accidentally escapes the barn and is captured by humans.
When the farmer puts a sign that says "Welcome Buyers", the animals fear that he is selling the barn to other people, so whenever someone comes to the barn, they use tactics to scare them away. But then they realize the Farmer's surname is Buyer and he is having a family reunion but they [accidentally] scared his family away.
Abby is excited that her cousin Veronica is coming to the barnyard for a visit, but it turns out Veronica, despite appearing to be nice on the outside, is actually using her beauty to manipulate the animals into doing things to please her.
When news anchor Hilly Burford is crushed covering a giant cheese curd that Otis made, the animals fill in for him on the news and 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.
When Otis accidentally blows up the barn, they audition for “Bling My Barn,” a home improvement show that fixes up barns for deserving families.
The animals turn the barnyard into a Wild West theme park to raise the Farmer's bail money (who got arrested because of Otis' antics) and decide to hire an actor to play the bandit. But instead of an actor, a real bandit shows up to pillage the town.
Pig writes a love letter to his favorite pastry treat, but Otis finds it and thinks Abby wrote it to him.
In order to get out of going to a "Brianna Texicanna" concert with Abby so he and his friends can go bowling, Otis lies and says he needs to celebrate “Happy Animal Fun Time Day” in which everybody must stay home to celebrate.
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.
When Otis injures himself, Pip takes over temporarily as 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.
The animals claim the farm as a protected habitat to prevent an interstate from tearing it down and disguise Freddy as a spotted three-toed ferret. But then they realize that this species is real, and a real female spotted ferret is shipped to the barnyard and Freddy falls in love with her. But the animals realize that female spotted ferrets eat male spotted ferrets when they marry, so the gang must get rid of her.
The animals must stand in for injured football players in a game after becoming the mascots for the team.
Otis is too lazy to do chores around the barnyard so he creates a clone of himself to do the work for him. Turns out the clone is a much smaller version of him. And when Mrs. Beady ends up capturing the clone, she is set to take him to a TV show so she can prove that animals can talk.
When responsibility is thrust upon Otis to watch the three kids of the barnyard, Joey the calf, Macy the lamb, and Boyle the chick, Otis loses them upon taking them around the big city.
When Snotty Boy's cousin Bernard stays at the Beady house and torments Snotty, he escapes and tries to seek refuge in the barnyard. So the animals must help Snotty to defeat Bernard so he could leave.
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. "Dr. Filly" is revealed to be an imposter donkey.
When animals go on a camping trip, Pip tells a scary campfire story about a witch. When they get lost and find an old woman's house with tons of sweets, Otis fears that this woman is indeed the witch from Pip's story.
The animals buy a security system for the barnyard, but it turns out that the system is doing more harm than good.
The animals liberate a show whale from a water park, but Otis has a lot more to go when the animals are being eaten by this whale.
Duke wants a playmate but no other animal wants to play with him, so the animals convince the farmer to get Duke a playmate. But everything turns out bad when the farmer brings Duke's arch-rival Baxter back to the farm, and Baxter causes trouble with the farmer but makes the farmer thinks Duke did everything, getting Duke in trouble.
Otis is knocked out and wakes believing that he is King Cudenhotep. The only way for him to get back to normal is if someone knocks him in the head again, but Otis has beaver guards that prevent others from getting too close to him.
The animals find an old safe in the barn that belonged to Everett's former owner Nebraska Schwartz. Everett doesn't remember the lock combination to open the safe, so Otis helps Everett recreate past memories of Everett's adventures with Nebraska Schwartz to help Everett recall the number.
Otis disguises himself as a TV chef to save Peck from being cooked after Freddy's recipe for a tofu rooster that is going to be cooked on the show. But the chef insists on using real rooster, and captures Peck.
When Pig cooks up what appears to be permanent glue, the animals try to sell the glue to make money. But they soon realize that the glue explodes two hours after it is applied.
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.
The animals get arrested when they are mistakened by the police for bandits disguised in animal costumes. Chained together, they try to escape so they can use a computer to find the real thieves.
Bessy is constantly rude towards the animals, yet she is rarely seen, so the animals wonder what she does when they don't see her, so they try to spy on her.
After Freddy gets struck by lightning, he becomes a genius and knows everything, so they get him to compete in a trivia show so they can win a million dollars. But then they realize that Freddy's intelligence is only temporary and he becomes stupid again after a prolonged period of time.
In a bid to collect the most Halloween candy and win a prize, Otis tops off the animals' trick-or-treat candy with a handful of candy from a hollowed-out pumpkin that legend says belongs to Hockey Mask Bob and reclaim his candy.
Otis and the gang go to an arcade so they can get tickets to buy a gaming console. But Snotty Boy and his friends also want the console so they have to compete to see who can get the most tickets first.
The farmer is in love with a woman who's a rodeo host and is interested in bull riders, so Otis pretends to be the farmer's bull so the woman would be impressed. But at the rodeo, Otis meets a much bigger bull who injures Otis so now the farmer has to ride the big (and dangerous) bull.
The animals climb a mountain to reach Bigfoot's home after Bigfoot gets in an accident.
The animals successfully pranks Mrs. Beady into taking a holiday. Now they no longer have to worry about getting caught by her, but now Otis experiences withdrawal symptoms because he is no longer able to prank her.
It's Christmas Eve and Santa Claus comes to visit the barnyard, but after Santa catches Ferret Fever from Freddy, the animals have to go deliver all the presents themselves.
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 and he goes out of control.
Duke is excited when his sister Stamps comes to visit, but is shocked when he realizes that Stamps is engaged to his arch-rival, Baxter.
Pip falls in love with a donkey named Prunella, but Bessy repeatedly tries to break the two up, leading to others to believe that Bessy loves Pip.
The clones Little Otis and Little Abby come back to visit the barnyard, but it becomes a problem because they never sleep so the animals couldn't sleep when they're here. In order to make them stop visiting, they try to create mini-clones of more animals so Little Otis and Little Abby can have friends. But things go awry when the owner of the Clone-a-torium plans to use those clones to expose the humans so they would know that animals can talk, and Otis and his friends must stop him from doing it.
Snotty Boy's clown dad comes to visit, leading into a battle against the fake dad (Otis) and the real one.
An ancient cave cow comes to attack the barn animals! Meanwhile, scientists kidnap Otis, thinking he's really Cave Cow.
Otis and his pals try to catch a leprechaun.
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.
Otis finds a giant chicken egg and decides to hatch it so they can have a fifth for polo. Only the giant chicken turns out to be a dinosaur! The animals immediately want to get rid of it, but Otis has paternal feelings and begs the animals to give him a chance. They relent, but the dinosaur quickly grows 1000 times its size and falls in love with Mrs. Beady!
Pig's mole subjects (from when he was Emperor of the Mole People for 45 minutes) have sought him out to return as their Emperor and defend them from Eric the Terrible, a verbally abusive worm.
Otis's former best friend named Eddie returns and tries to get rid of Pip, and Otis and his friends must stop him.
Mrs. Beady has no choice but to move with the barnyard animals after being kicked out of her house.
In this series finale, While creating a fake alien news story to scare away Mrs. Beady, Otis accidentally attracts actual space aliens bent on conquering Earth. Otis tries to stall them at the barnyard while he tries to find their weakness.
When the farmer's away, all the animals play, and sing, and dance. Eventually, though, someone has to step in and run things, a responsibility that ends up going to Otis, a carefree cow.