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

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.

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 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.

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 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 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.

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.

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.

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.

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.

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 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.

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' negligence causes Pip to get captured by Snotty Boy, who plans on feeding him to his new pet snake (who talks exactly like him).

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.

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.

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.

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.

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.

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' 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