Shaun, an adventurous sheep at Mossy Bottom Farm, finds himself weary of the mundane farm life. In a bid for freedom, he devises a clever scheme to trick the farmer into falling back asleep by having him count sheep repetitively. Unfortunately, their plan takes an unexpected turn when the caravan used to put the farmer to rest rolls away, transporting him into the heart of the city. In hot pursuit is Bitzer, the farmer's loyal dog.
After suffering a head injury, the farmer is taken to a hospital where he is diagnosed with amnesia. Upon his release, he stumbles into a hair salon. Acting on a distant memory of shearing his sheep, he unexpectedly ends up giving a celebrity a trendy haircut, which quickly skyrockets his popularity as a stylist, earning him the moniker "Mr. X."
Back at the farm, the sheep struggle to adjust to life without their farmer. Determined, Shaun hops onto a bus heading to the city, only to find his entire flock has followed him on a second bus. They don disguises to blend in and search for the farmer, but trouble brews when Shaun is captured by the grumpy Animal Control officer, Trumper. Reunited with Bitzer in the animal lock-up, the duo receives an unexpected assist from a resourceful stray dog named Slip, and together, they hatch an escape plan while managing to outsmart Trumper.
The adventure leads them to the farmer, but disappointment sets in when he fails to recognize his beloved sheep. Shaun, Bitzer, and the flock seek refuge in a dark alley, where they discover clues indicating the farmer might regain his memories. They formulate a plan to put him to sleep once more and safely return him to the trailer on a makeshift pantomime horse. However, their efforts are thwarted when Trumper attacks them with a taser, leading to a thrilling chase down the alley.
As the climax unfolds at the farm, the group takes cover in a shed while Trumper, commandeering the farmer's tractor, attempts to push it into a looming rock quarry. Just as things seem bleak, the farmer awakens, his memories flooding back, and together with the animals, they thwart Trumper's plans. In an explosive finale, teamwork prevails, and a bull launches Trumper into the air, sending him crashing into a mud pile.
In the aftermath, the bond between the farmer and the animals deepens, leading to a newfound appreciation for each other. The very next day, the farmer surprises everyone by cancelling their usual chores for an official day off. As the story wraps up, we witness a transformation where the animal-control service becomes an animal protection center, while Trumper finds himself in an amusing predicament, dressing as a chicken to help promote a local restaurant. In a delightful mid-credit scene, the farmer watches a bewildering news report revealing the chaos he inadvertently slept through during his escapade, leaving both him and his animal companions astounded.
