In the series finale, Otis orders a satellite dish online in order to watch monkey boxing from Rio. Mrs. Beady sees this and believes that he is secretly signaling Aliens. Otis finds out and tries to prank Mrs. Beady with a fake alien invasion broadcast. This broadcast is sent to real aliens who are attracted to Earth and plan to conquer and destroy the planet. The animals must stop and stall them while they figure out their weakness.
Pig's mole subjects (from when he was Emperor of the Mole People for 45 minutes) have sought him out to return as their Emperor and defend them from Eric the Terrible, a verbally abusive worm and with the mole people around the barnyard, they can't get Pig to hang out with them because they keep shocking them when they are near Pig.
Otis finds a giant chicken egg and decides to hatch it so they can have a fifth for polo. The giant chicken egg turns out to be that of a dinosaur, which proceeds to wreak havoc wherever it goes. The animals want to get rid of it, but Otis has paternal feelings and begs the animals to give him a chance. They relent, but things truly go awry when the dinosaur quickly grows a thousand times its size and falls in love with Mrs. Beady.
Otis and his friends become cops after another cop gets injured, and they try to solve a crime that is about stealing in a donut store. They find the suspects are Mrs. Beady, Snotty Boy and the Farmer. They try to interrogate them, but they're all innocent. They then learn that Pig is the real thief because he wore a burglar costume every time he goes to get donuts for his friends.
The leprechaun steals the farmer's potatoes after Otis sprayed the potatoes, Otis and pals must stop him before the farmer goes bankrupt and the animals for less outlet. Unfortunately, also, the leprechaun turns Freddy and Peck into shamrocks and Pig into a corn beef sandwich head. Luckily, Otis gets an idea to cut out the middle man meaning to find the leprechaun's gold instead of catching him to surrender.
An ancient cave cow comes to attack the barn animals! Meanwhile, scientists kidnap Otis, thinking he's really Cave Cow.
While trying to escape Snotty Boy, the animals run over Snotty's clown father. His dad survived, but has lost a lot of hilarity and Pig takes him into surgery. Otis disguises himself as Snotty's father to distract him while he recovers and becomes a cool dad to Snotty Boy. Only Snotty comes to love and admire Otis in a way he never did for his lame clown father. Otis has to think fast before he ruins this miserable family.
A group of Canadian Crows want to steal the corn from the barnyard, but after repeated failed attempts, they decide to give the animals a fake treasure map to distract them from guarding the corn.
When a beautiful she-donkey named Prunella takes an interest in Pip, Bessy suspects ulterior motives and follows them on their dates, causing the other animals to accuse her of being jealous.
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.
The animals successfully prank Mrs. Beady into taking a holiday. Now, they no longer have to worry about getting caught by her, but now Otis experiences withdrawal symptoms because he is no longer able to prank her.
The animals climb a mountain to reach Bigfoot's home after Bigfoot gets in an accident.
Mrs. Beady has no choice but to move with the barnyard animals after being kicked out of her house and being mistreated by Mr. Beady's mother, Mother Beady.
Otis' old best friend, Eddie comes to visit. Otis is mad because Eddie stole his product idea for pizza flavored gum. Eddie claims to have seen the error of his ways and wants new product ideas. Eddie starts hanging out with the gang and wins them over, except for Pip, who is suspicious. Pip then finds out that Eddie is just a sleazy, backstabbing jerk and reveals this to the gang. The gang decides to get rid of him by having the crows send Eddie flying off in a car made from cobs of corn from the field. Unfortunely, Eddie manages to make a bundle off the car, leaving the others in shock, except for Pig, who stupidly thinks Eddie won.
The farmer is in love with a woman named Branco Betsy who's a rodeo host and is interested in bull riders, so Otis pretends to be the farmer's bull so Branco Betsy would be impressed. At the rodeo, however, Otis meets Psycho, a much bigger bull, who injures him, so now the farmer has to ride Psycho, the big (and dangerous) bull.
Duke is excited when his sister Stamps comes to visit, but is shocked when he realizes that Stamps is engaged to his arch-enemy, Baxter. However, the animals learn that Baxter is after Duke and Stamps' uncle's priceless dog bone collection. When they try to frame Baxter for chewing up a couch at his bachelor party (so that Stamps will dump him because she hates couch-chewers), Duke beats him to it and now scolded in front of Freddy and Peck. So at the altar, Duke tells Stamps about Baxter going after the dog bone collection, she dumps Baxter and he is launched in the field.
Otis and the gang go to an arcade so they can get tickets to buy a gaming console. Snotty Boy and his friends also want the console, however, so they have to compete to see who can get the most tickets first. When the animals get the game console, they end up giving it to a little boy who begs for the console and turns out to be a midget. The arcade is eventually destroyed when Pig accidentally shines his pocket mirror in a animatronic fox's eyes which had a 3rd setting called "Destroy Humans."
After Otis accidentally breaks up Peck's body with a hammer, he rebuilds Peck by adding robot parts to him so he can be a big help around the barnyard, but things go awry when Peck's circuits get overloaded after Otis puts pizza inside him and he goes out of control.
After Freddy gets struck by lightning, he becomes a genius and knows everything, so they get him to compete in a trivia show so they can win a million dollars. They realize that, unfortunately, Freddy's intelligence is only temporary and he becomes stupid again after a prolonged period of time. So the animals make an electrical system to make Freddy smart with each shock. But the problem is, every time a question is announced, he keeps getting dumb again and again. Frustrated that he keeps getting dumb, Freddy goes backstage and shocks himself at high velocity and dreams that he meets with Albert Einstein who gives him the answer to the final question which is actually incorrect so Freddy curses Albert Einstein for making him lose.
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.
Otis convinces his college buddies Donner and Blitzen to stop by the barnyard on Christmas Eve. During the visit, Otis accidentally gives Santa a cup belonging to Freddy, who is sick. When Santa comes down with Ferret Fever and can't finish his rounds in the county, which turns out to be his last stop on his Christmas Eve rounds, then Otis and the animals vow to make toys and deliver them by midnight to save Christmas. Meanwhile, Snotty Boy, not knowing he’s on the naughty list, really wants a Red Rider BB Taser that Santa doesn't bring him every year. So he sets a trap for Santa to make sure he brought his present.
The animals get arrested when they are mistakened by the police for bandits disguised in animal costumes. Chained together, they try to escape so that they can use a computer to find the real thieves. But when they do catch the real thieves, the police says due to budget cuts, they aren't any keys to free them from their chain, so now they're stuck chained together
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 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 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.
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 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.
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 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.
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.
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 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.
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 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 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 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.
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 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.
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.
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.
Pig writes a love letter to his favorite pastry treat, but Otis finds it and thinks Abby wrote it to him.
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 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.
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 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.
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.
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.
