In order to celebrate Otis' birthday the animals trick Farmer into going to Turnip-Con for the weekend. However his plans hit a snag when that very same weekend the Beady's nephew, Eugene, comes for a visit.

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. They ended up landing in a golf course and mistaken it as their new paradise.

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 is bored of Abby's book club, so he releases Wild Mike from a cage so they can have a dance party, but things get out of control when Wild Mike accidentally escapes the barn and is captured by humans to use on a dancing TV show.

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. Then, though, they realize the Farmer's surname is Buyer and he is only having a family reunion. So they returned the Farmer's family to the barnyard just in time for the reunion.

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.

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 Otis accidentally blows up the barn with an atom smasher he accidentally received in the mail, they audition for "Bling My Barn," a home improvement show that fixes up barns for deserving families. But when they dress up Pig as a baby, he discovers the perfect family they're competing against, he tries to warn the gang but they ignore him thinking he's throwing a tantrum, so he runs away forcing them on a wild goose chase to catch him. When they finally caught Pig, he shows them the perfect family, so they drop out of the contest and use the material from the farmer's house to rebuild the barn.

The animals turn the barnyard into a Wild West theme park to raise the Farmer's bail money (who got arrested because of Otis wearing a viking helmet and mooning a cop) and decide to hire an actor to play the bandit. Instead of an actor, unfortunately, a real bandit shows up to pillage the town. So Pig comes to Otis' rescue with unicorns from the unicorn theme park to stop the bandit from attacking the barnyard.

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 to beat a rival farm, Otis lies and says he needs to celebrate "Happy Animal Fun Time Day" in which everybody must stay home to celebrate. But Abby believes him and decides to cancel going to the concert and stay home to celebrate too. So Otis distracts her with the holiday's activities so that he can join with his friends at bowling and Abby doesn't see that he lied to her.

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.

Otis is too lazy to do chores around the barnyard so he creates a clone of himself to do the work for him. It 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, after Abby and Bessy read story time, Otis loses them upon taking them around the big city when Otis and the gang had to remove a chip from Freddy's skin to keep Abby and Bessy from finding out where they are. So Otis and the gang stage a fake robbery to reunite with the kids after a cop finds them and about to take them to the station. But soon the kids call Abby & Bessy to pick them up. On the way back to the barnyard in a helicopter, Bessy tells them about Otis being a lair and after each line, she punches Otis and with him asking for a parachute to bail the helicopter.

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 then 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. 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.

When the 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 called The Barn Buddy (voiced by Gilbert Gottfried) for the barnyard, but it turns out that the system is doing more harm than good.

After Freddy's recipe for a tofrooster that is going to be cooked on the show, things get worse when Chef Big Bones (voiced by Jim Cummings) insists on using a real rooster, and captures Peck, so Otis disguises himself as a chef to save Peck from being cooked.

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.

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 is knocked out and wakes believing that he is King Cudenhotep. The only way for him to get back to normal before the farmer comes back is if someone knocks him in the head again, but Otis has beaver guards that prevent others from getting too close to him. When they finally turn Otis back to normal, the farmer see them but get hit on the head believes he is Ben Franklin.

The animals liberate a show whale from a water show at a fair, but Otis has a lot more to go when the animals are being constantly 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. 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 must stand in for injured football players in a game and the coach’s mother to like him after becoming the mascots for the team.

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.

n 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 hollow tree that legend says belongs to Hockey Mask Bob who always gets his candy stolen and vows to return for revenge and reclaim his candy.