A lonely boy named Danny Garrison befriends the rat that leads the swarm of trained/telepathic rats found in Willard. This rat, whom the boy names Ben (after he hears about the leader of a flock of killer rats), becomes the boy's best friend and keeps his spirits up in the face of bullying and his terrible illness.

However, the balance of power between Danny and Ben begins to shift, with Ben beginning to control the swarm becoming increasingly irrational and violent. Ben becomes violent when the townfolk use pesticide and kill his partner "Socrates".

Eventually, the police destroy many members of the rat colony. However, Ben survives. The film closes with Danny, determined not to lose his friend, tending to a badly injured Ben.