The movie opens with a recap of the ending of the first film, where Willard Stiles is killed by his rats after he tries to kill them and Ben. Police arrive at the Stiles house; two officers stay behind, and one is attacked and killed by the rats while the other finds Willard’s body. Detective Clift Kirtland, Joseph Campanella, orders an exterminator to wipe out the rat population, but Ben overhears the plan and warns the rest of the colony. With a quiet, stubborn resolve, Ben and the other rats slip away into the sewer, seeking safety beneath the city.
A lonely boy named Danny Garrison, Lee Montgomery, who has a severe heart condition, lives with his sister Eve Garrison, Meredith Baxter, and his mother Beth Garrison, Rosemary Murphy. Danny meets Ben while he’s playing with marionettes in his workshed, and the rat leader quickly becomes the boy’s best friend. That same day, Ben and the rats crash a food truck, forcing the driver to crash and killing another driver, an event that foreshadows the escalating danger to the neighborhood. Later, Danny plays a tune he composed on the piano for Ben, a small moment of connection that underscores the unusual bond forming between human and animal.
As night falls, Ben’s colony spreads through the town in a determined hunt for food, invading a grocery store and leaving destruction in its wake. Police officers and detectives step up their efforts, using poison and traps to try to quell the rat menace, while Danny warns Ben about the traps and the risk they pose. A bully at school tries to torment Danny, only to be confronted by Ben and the other rats, who bite him in the legs and drive him away. The bully returns with his mother and the police, and Danny leads them to the workshed, presenting a marionette that resembles Ben as a plea for mercy. The visitors leave, unsettled by the strange friendship between boy and rat.
Yet the situation continues to deteriorate as Ben’s colony grows more violent in its search for sustenance, and several people lose their lives in the chaos. The police eventually descend into the sewers and unleash flamethrowers and shotguns in an effort to wipe out the rats, trapping the creatures underground. Ben somehow survives the brutal assault and crawls back to Danny, wounded but alive. In the aftermath, a tearful Danny tends to his injured friend, his resolve strengthened by the near-loss of his closest companion and his vow not to let go.
