Shaun, a mischievous sheep living with his flock at Mossy Bottom Farm, is bored with the routine of life on the farm. He concocts a plan to have a day off by tricking the farmer into going back to sleep by counting his sheep repeatedly. However, the caravan in which they put the farmer to bed accidentally rolls away, taking him into the city. Bitzer, the farmer's dog, chases after him.
Shaun the Sheep and his herd are enthralled when an alien crash-lands near Mossy Bottom Farm, but little does Shaun know that a sinister alien-hunting agency is hot on their trail.