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.

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.

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.

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.

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.

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.

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.

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.

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 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 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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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.