BEN

The movie begins 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 scene and find Willard dead. Two police officers stay at the Stiles house where one of them is attacked and killed by the rats while the other finds his body. A police detective named Clift Kirtland orders to have an exterminator to kill the rats, but Ben hears this and tells the other rats. Together, Ben and the other rats go into the sewer.

A lonely boy named Danny Garrison, who has a severe heart condition, lives with his sister, Eve, and his mother, Beth. Danny finds and befriends Ben while playing with marionettes in his workshed, and Ben becomes the boy's best friend. Later that day, Ben and the other rats attack a food truck, causing the driver to crash and kill another driver.

The next day, Danny plays on the piano a song he has created for Ben. Later that night, Ben and the other rats invade a grocery store for food and destroy the entire store. Police officers and detectives are now trying to kill the rats with poison and traps in the neighborhood, but Danny tells Ben about the traps set up by the police. Just then, a bully comes to make fun of Danny, but Ben and the other rats attack the bully by biting him in the legs. The bully gets scared and runs away. Danny thanks Ben and the rats for helping him with the bully. The bully comes back with his mother and the police. The police tell Danny they want to see Ben, so Danny brings them to the workshed and throws at them a marionette he made that looks like Ben. The police, with the bully and the bully's mother, leave the workshed.

However, things gradually take a downhill turn as Ben's colony becomes violent in its search for food, resulting in several deaths. Eventually, the police go into the sewers and kill the rats with flamethrowers and shotguns after trapping them there, but Ben somehow survives the slaughter and makes his way back to Danny, wounded but alive. A tearful and overjoyed Danny tends to the injured Ben, determined not to lose his best friend.

After a citywide rat hunt, Ben survives the extermination and returns wounded to Danny, who cares for his injured friend.

The ending underscores the resilience of Ben and the enduring, if unsettling, friendship between boy and rat. Despite the city's efforts to eradicate the threat, the bond between Danny and Ben survives, suggesting that some connections—however unlikely—can outlast even the most determined opposition.