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.

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.

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.

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

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.

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.

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 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 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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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.

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.

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 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.

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.

Bessy is constantly rude towards the animals, even though she is barely seen. The animals wonder what she does when they don't see her and try to spy on her.

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 Pig, Pip, Freddy, and Peck so Little Otis and Little Abby can have friends. A problem arises when the owner of the Clone-a-torium plans to use the clones to expose the humans so they would know that animals can talk, and Otis and his friends must stop him from doing so.