An ancient cave cow comes to attack the barn animals! Meanwhile, scientists kidnap Otis, thinking he's really Cave Cow.

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.

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.

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 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.

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.

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.

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.

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.

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. Things take a turn for the worst when Otis says he is leaving for a magical land but Pig believes it and wants to go with him. All of the sudden, the real Mr. Wiggleplix comes alive and stops Otis from impersonating him.

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.

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.

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 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 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.

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.

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 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.

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.

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.

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 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.

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.