The film opens in Mossy Bottom Farm. Shaun, Timmy (both Justin Fletcher), Bitzer, The Farmer (both John Sparkes), and the rest of the flock wake up and get ready to do their chores. The sheep are growing pumpkins in time for Halloween, keeping them hidden for protection.
The farm is visited by a Vet (Nina Sosanya), whom The Farmer is smitten with. Bitzer and the sheep hide from her to avoid getting their medicine, but she is able to quickly find them (except Bitzer) and administer the medicine into their mouths. The Vet also appears to return The Farmer’s feelings. She plans to invite him to a Halloween event (one that he was already planning to invite her to), but The Farmer gets yanked away by his goat. He ends up crashing into the flock’s pumpkin patch, destroying all the gourds, to the dismay of the sheep.
Shaun finds a science book and comes up with an idea to produce large pumpkins quickly to replace the ones that were ruined. He creates a potion like a mad scientist and adds it to the seeds after planting them. Since Shaun put it inside an empty container of hair growth formula, Bitzer returns it to The Farmer, who was hoping to regrow his hair to impress The Vet. He adds some to his head before going to bed.
In the morning, The Farmer has grown more hair on his head, and then on his face. The flock’s pumpkins have also grown rapidly. The Farmer puts on an ill-fitting leather outfit to meet The Vet and invite her to the Halloween event. However, Shaun sees that the pumpkins are STILL growing.
At The Vet’s office, The Farmer sees that the hair on his face, head, and body are growing even larger. He is forced to hide from The Vet, and The Farmer’s entire body becomes covered in hair. He accidentally steps in cement, and the stuff that hardens on his feet make his footsteps loud and thunderous. The Farmer returns to Mossy Bottom and frightens the other animals.
Shaun and the flock hide in the bathroom, while Bitzer hides elsewhere. The Farmer enters the bathroom to try and shave himself. Shaun sees his glasses and quickly realizes who it is, alerting the other sheep but keeping it from Bitzer.
The sheep go to a cave where they find The Farmer having failed to remove his hair, because it just grows back right away. When he rips it off, he lets out a loud yell that is heard in Mossingham, frightening the townsfolk. After The Farmer leaves and ends up in town, he is exposed after posing as a statue, and everyone freaks out. The Shopkeeper (Paul Whitehouse) leads the mob against The Farmer. Meanwhile, The Vet sees The Farmer’s big footprint and begins to believe that Bigfoot is in town, and she hopes to send the “beast” to an island with other sasquatches. When Bitzer finds the cave and sees The Farmer’s glasses, he assumes his master was eaten, until Shaun eventually tells him the truth.
The Farmer gets incapacitated, and The Vet manages to get him on a boat. Shaun leads the flock to the dock and distract the crew so that they can get the crate that The Farmer is stashed in. Bitzer tries to get into the control seat, but he gets stuck in a stink gas that the sheep threw in, and he gets the boat moving. The sheep get the crate off the boat before it sails, but when they open it, it’s full of fuzzy dolls, and The Farmer is still on the boat. The sheep leave, defeated.
When they get back to the farm, the flock sees that the pumpkins have grown to such a colossal size that they have destroyed parts of the farm. Shaun is shut out by the other sheep. He goes back to the cave, where the others meet him later. They find The Farmer’s phone and see numerous missed calls from The Vet. Shaun remembers that they shared a connection, so he gets an idea. He draws a picture on the cave wall to try and explain to The Vet that the “beast” is really The Farmer. She gets it and hops on a boat to go after him, with Shaun sneaking onboard. The Vet helps other stuck animals in the ocean, who end up helping her and Shaun catch up to the ship. The Vet is able to free The Farmer, and everyone sails back to land.
Shaun returns to the barn and gathers the flock to create an antidote for The Farmer. The townspeople spot The Farmer and chase him to the windmill where Shaun is setting up the antidote, and The Shopkeeper even tries to prevent The Vet from helping. The Farmer gets stuck on the windmill until Timmy and the other sheep arrive with a giant pumpkin and make it look like it eats The Farmer. Shaun gets the antidote ready and sprays it on The Farmer, removing all his hair and turning him back to normal. The Vet then pushes the giant pumpkin to scare away the townsfolk, and it grabs The Shopkeeper in its mouth.
Later on, The Farmer and The Vet get together to go to the Halloween event. Shaun, Bitzer, and the flock fashion the pumpkins into giant Jack-o-lanterns, and then they have a party in the barn.
During the credits, a crow is seen drinking what’s left of the growth formula, and it starts to glow ominously…
