While aboard a houseboat on Crystal Lake, teenager Jim Miller tells his girlfriend Suzi the legend of Jason Voorhees, before playing a prank on her with a hockey mask and a prop knife. The boat's anchor damages some underwater cables that shock Jason's corpse, which is still chained at the bottom of the lake, and revive him. He sneaks on board, takes the mask, and kills Jim with a harpoon gun before impaling Suzi.
The next morning, the SS Lazarus is ready to set sail for New York City with a graduating senior class from Lakeview High School, chaperoned by biology teacher Dr. 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. Jarrett with her guitar. That night, a young boxer who lost his match to champion Julius Gaw is killed by Jason in the ship's sauna. Rennie, searching for her pet Border Collie Toby, discovers prom queen Tamara Mason and her friend Eva Watanabe doing drugs. McCulloch nearly catches them moments later and Tamara pushes Rennie overboard, believing that she told on them. She then uses video student Wayne Webber to record McCulloch in a compromising situation with her but rejects Wayne's advances afterward. Jason kills Tamara with a shard of broken mirror after she showers.
Rennie sees visions of a young Jason throughout the ship. Jason kills Captain Robertson and his first mate. Rennie's boyfriend and Captain Robertson's son, Sean, discovers them and tells the others before calling for an emergency. Eva finds Tamara's body and flees. Jason chases Eva into the disco room, where he strangles her to death on the dance floor. The students agree to search for Jason while McCulloch decides that the deckhand is responsible. However, the deckhand is found with a fire axe in his back. Jason tosses student Miles Wolfe into the radio transmitter tower to his death, and Julius is knocked overboard. In the hold of the ship, Wayne comes upon J.J.'s body and is thrown into an electrical box by Jason. Wayne's corpse catches fire and causes the ship to take on water. With the other students that were left in the disco room seemingly dead, McCulloch, Van Deusen, Rennie, and Sean escape aboard a life raft and discover that Toby and Julius are still alive.
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 fights Jason but becomes exhausted after Jason does not go down and gets decapitated by a single punch from Jason. 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 police 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 drowns him in a barrel of toxic waste.
Jason chases Rennie and Sean into the subway, where Sean incapacitates Jason by pushing him onto the third rail. When Jason revives, he chases them through Times Square to a diner, and then to the sewers where they encounter a worker. He warns them that the sewers will be flooded with toxic waste at midnight. Jason appears, kills the worker and knocks Sean unconscious. Rennie throws a vat of toxic waste into Jason's face. She and Sean climb a ladder as Jason staggers after them. The sewers flood, and Jason, reminded of his childhood drowning, vomits water. The waste water overcomes Jason, causing his face to melt away. When the water recedes, Sean and Rennie witness what appears to be Jason as an unconscious child. Sean and Rennie make their way back to the street where they are reunited with Rennie's dog Toby in Times Square.
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