One year after the previous film, two graduating high school students are aboard on a houseboat. Jim tells his girlfriend Suzy the legend of Jason Voorhees, before playing a prank on her with a hockey mask and a fake knife. The boat sails over some underwater cables, which electrocute Jason’s corpse and cause his resurrection. He sneaks on board and stabs Jim with a harpoon barb before impaling Suzy, who tries to hide from him.
The next morning, the SS Lazarus is ready to set sail for New York City with a graduating senior class from Lakeview High School and chaperoned by biology teacher Charles McCulloch and English teacher Colleen Van Deusen. Van Deusen brings McCulloch’s niece Rennie along for the trip despite her aquaphobia much to his chagrin. Jason sneaks on board and kills rock star wannabe J.J. with her guitar before hiding in the bowels of the ship. That night, after a boxing match, a young boxer who lost to champion Julius Gaw is killed when Jason slams a sauna rock into his abdomen while Rennie, searching for her dog Toby, discovers prom queen Tamara and Eva doing drugs. McCulloch nearly catches them moments later and Tamara pushes Rennie overboard, suspecting she told on them. She then uses video student Wayne to record McCulloch in a compromising situation with her, but rejects Wayne’s advances afterward. Tamara is killed by Jason when she goes to take a shower. Rennie begins seeing visions of a young Jason throughout the ship, but the others ignore the deckhand’s warnings that Jason is aboard. Jason kills Captain Robertson and his first mate. Robertson’s son Sean discovers them and tells the others before calling for an emergency stop. Eva is strangled as she tries to flee from Jason. The students agree to search for Jason while McCulloch decides that the deckhand is responsible; however, the deckhand is discovered with an axe in his back. One of the students, Miles, is killed by Jason and Julius is knocked overboard. Wayne discovers Jason in the hold of the ship and is thrown into an electrical box; his corpse catches fire and begins a chain of events that causes the ship to sink. With the other students dead, McCulloch, Van Deusen, Rennie and Sean escape aboard a life raft, and discover Toby and Julius are alive as well.
They row to New York where Jason stalks them through the streets. Rennie is kidnapped by a pair of junkies and the group splits up to find help. Julius tries to fight Jason with his boxing skills but is decapitated by a single punch. Rennie escapes from Jason when he kills the punks that kidnapped her.
She runs into Sean and they reunite with the teachers and the police before Jason kills the officer who is helping them. Rennie crashes a car after a vision of Jason distracts her. Van Deusen is incinerated in the car when it explodes, and it is revealed that McCulloch is responsible for Rennie’s fear of water, having pushed her into the lake as a child. They leave him behind and Jason kills him by drowning him in a barrel of waste.
Jason chases Rennie and Sean into the subway where Sean incapacitates him by knocking him onto the electrical third rail. He is revived again and chases them through Times Square where they try to escape through a diner. They flee into the sewers and encounter a sewer worker. He warns them that the sewers will be flooded with toxic waste at midnight before Jason appears and kills him. Sean is injured and Rennie draws Jason off, wounding him with a splash of acidic waste.
She and Sean climb the ladder as the sewers flood, Rennie sees a child-form of Jason as the two of them escape to the street. Rennie and Sean reunite with Toby who had run away earlier, and walk off into the city.