In the quaint town of Mossingham, a man named John and his loyal Border Collie, Bingo, stumble upon an extraordinary event—a UFO landing. Meanwhile, at the bustling Mossy Bottom Farm, Shaun the Sheep and his flock find themselves engaged in a series of risky escapades, consistently thwarted by the ever-watchful sheepdog, Bitzer. After the Farmer places a ban on their barbecue dinner, Shaun hatches a plan to order three pizzas. However, when the delivery arrives, they are disheartened to find the boxes utterly empty.
Upon waking the next morning, Shaun notices a peculiar trail of pizza crusts that leads him to an unexpected encounter. He meets an enchanting visitor named Lu-La, a tentacled, dog-like alien hailing from the planet To-Pa, who possesses the ability to mimic sounds and levitate objects. Eager to introduce her to the flock, Shaun’s attempts culminate in chaos when Lu-La inadvertently wreaks havoc on the farmer's combine harvester, transforming the field into a series of unintended crop circles.
Seizing the buzz surrounding recent alien sightings, the Farmer resolves to launch an alien-themed amusement park dubbed "Farmageddon," aspiring to profit enough to purchase a new harvester. Meanwhile, the leader of the Ministry of Alien Detection, Agent Red, who has been fervently hunting for concrete evidence of extraterrestrials since witnessing two aliens in her childhood, embarks on an investigation into the UFO reports.
As Lu-La and Shaun pursue the UFO, they are followed by Bitzer, who is humorously clad in an alien costume while distributing flyers for "Farmageddon." Inside the UFO, Lu-La shares her memories with Shaun, revealing that she is actually a child who accidentally launched her parents' spacecraft during playtime. Recognizing the need for an egg-shaped device she inadvertently dropped, they endeavor to recover it. However, M.A.D. mistakes Bitzer for an alien, leading them to capture the UFO, along with Shaun and Lu-La still aboard.
At their hidden base, Shaun and Lu-La cleverly manage to sneak out and reclaim the device, successfully rebooting the spaceship. They aim for To-Pa, but, disregarding Bitzer's warnings, Shaun's enthusiasm leads to a crash landing back at the farm. Devastated by the wreckage of the UFO, Lu-La feels despondent. However, undeterred, Shaun uncovers that their device can emit a distress signal if they reach a lofty position. Together, they plot to ascend the Farmer's "Farmageddon" theme park tower to send a call for help.
With assistance from the flock and Bitzer, Shaun and Lu-La scale the tower as the Farmer hosts a spectacle at the theme park. As chaos unfolds, Agent Red pursues them wielding a mech suit. Displaying bravery, Shaun sends Red tumbling off the tower and successfully transmits a distress signal to To-Pa. Lu-La's parents, Ub-Do and Me-Ma, promptly arrive to reunite with their daughter. In a surprising turn, Red also acknowledges the aliens, recalling the beings she witnessed in her youth. Bidding farewell, Shaun, Bitzer, and the flock send the visitors off, while the "Farmageddon" theme park thrives on the pops of excitement surrounding the ordeal, all perceived as part of the park’s special effects.
In the mid-credits scene, Shaun, Bitzer, and the entire flock enjoy a lively game of frisbee, oblivious to the Farmer testing his new harvester nearby. Chaos ensues as the frisbee becomes ensnared in the machinery, leading to an explosive mishap.
The post-credits offer a humorous twist—one of the hazmat officials enters a dimly lit room featuring a piano. Upon removing his hazardous suit, he is revealed to be Brian Cox, attempting a rendition of "Things Can Only Get Better," only to be interrupted by Timmy, who unplugs the piano and hushes him.
