Two teenagers named Jim Miller and his girlfriend named Suzy Donaldson, are sailing Jim's boat on Crystal Lake when they pass by the abandoned camp.
As Jim tells Suzy the legend of Jason Voorhees, the boat's anchor catches onto a power cable which it drags onto the comatose body of Jason, shocking him back to life.
After scaring Suzy with a replica of Jason's hockey mask, Jim is killed when the freshly revived Jason eviscerates him with a harpoon gun before taking the mask for himself. Though Suzy tries to hide in one of the boat's cargo holds, Jason finds her and fatally stabs her to death with the harpoon.
The next day Charles McCulloch and Colleen Van Deusen take their students Rennie Wickham, Sean Robertson, Julius Gaw, Tamara Mason, Eva Watanabe (Kelly Hu), Wayne Webber, Miles Wolfe, and J.J. Jarrett on the S.S. Lazarus for a cruise to New York City. Unbeknownst to them, Jason has stowed away on the boat as well and begins a new killing spree when he hits J.J. by the head with her own electric guitar like a pumpkin.
Rennie and her dog Toby see a vision of the young Jason Voorhees in the window, and Toby runs off. Rennie goes looking for him and walks by Tamara and Eva, who are doing drugs. Shortly after they are caught by Charles, and Tamara thinks that Rennie told on them. As revenge, she pushes Rennie (who is afraid of the water) over the side of the boat. She is nearly drowned by the younger Jason before she is rescued by Colleen and Sean. The ship's deck hand (who is quite similar to that of Crazy Ralph) is constantly talking about Jason (and that everybody is doomed).
After a fight with Julius, an unnamed male boxer goes to a sauna to relax, and is killed by Jason, who uses one of the sauna rocks and plunges it into his abdomen. Later, he kills Tamara with a mirror shard in cold blood, and then murders Jim "James" Carlson and Sean's father named Admiral Robertson (killing Jim by stabbing him with a harpoon and killing Admiral Robertson by slitting his throat).
Charles does not believe that Jason has returned from the dead and is aboard the ship, but Julius does, so he takes charge and splits up with several students, armed with weapons and searching for Jason. Jason strangles Eva to death. While Wayne is searching for Jason, he loses his glasses, and accidentally shoots a crew member before Jason comes and electrocutes him. He then triggers the fire alarm.
Charles thinks it is a false alarm caused by the deck hand, whom he blames for the murders of his students, suspecting that he wants to cause panic. So he takes a flare gun and searches for him. While Miles is searching for him, Jason pops out of nowhere and gives chase, which leads up to a ladder. Jason then pops up on that ladder and throws Miles onto the radio antennae (which he disabled earlier) like a rag doll, killing Miles. Julius then comes up to find Miles dead, while Jason catches him off guard and throws him into the ocean.
When Charles finds the deck hand, he collapses to the ground dead with an axe in his back. Rennie, Sean, Colleen, Charles, and Toby get on a lifeboat and abandon the ship. Julius also gets onto the boat as well. Soon they finally reach New York.
Jason reaches New York shortly after they do, and sees a giant hockey billboard with a hockey mask on it. Looking at it, he tilts his head to the side as if to say "Is that me?". While they are wandering a deserted area, two gangsters named Homes and Jojo rob them, scare Toby away, and take Rennie away from them, threatening to kill her if they follow.
They inject her with heroin, then start trying to rape her, but Jason kills Homes by stabbing him with the empty heroin syringe. Jojo then comes, stating he forgot his wallet, then gets approached by Jason. He then tries to fend him off by shooting him, but Jason keeps approaching him, as if the bullets were nothing. Soon after, Jason grabs and bashes Jojo's head against a massive pipe like a watermelon, breaking the pipe and killing Jojo. Rennie then escapes while Jason looks on and starts after her.
While Sean finds Rennie and takes her back to Charles and Colleen, Julius encounters Jason on the roof of a building and fights him with his boxing skills, hoping to defend himself from the cold-blooded killer. Julius throws punches at Jason for exactly one minute and sixteen and a half seconds, before tiring himself out. Jason, walking backwards without retaliation while allowing Julius to punch him, suffers no damage at all and punches Julius head off. Rennie, Sean, Charles and Colleen find a cop, who places them in the back of his car.
But, when he gets in the front, the light comes on and they see Julius' severed head in the front. The cop then tries to call for backup, but he is quickly killed by Jason. Rennie drives the police car towards Jason, intending to hit him, which she successfully does, but after turning left into another alley the girl steers away when she sees the younger Jason ahead and crashes the car into a brick wall. Rennie, Sean and Charles manage to get out just in time but Colleen doesn't, and she dies right after when the car explodes.
Rennie remembers Charles pushing her into Crystal Lake, trying to teach her how to swim, and she was pulled underwater by a younger Jason. Rennie runs away and Sean goes after her, demanding Charles to stay away from her. Charles briefly stays behind and Jason gets up, and only now does Charles realize his true identity before Jason chases after him, throws him through a window like a rag doll and drowns him upside-down in a barrel of toxic sewage, killing him instantly. Jason then chases after Rennie and Sean, and they enter the subway, where Jason is electrocuted on train tracks, but survives.
While chasing Rennie and Sean, he kicks four punks' boombox radio over, and they get aggressive toward him, but he turns around and lifts up his mask (he is facing away from the camera so the audience does not see his face), and the punks all run off before Jason resumes his chase after Rennie and Sean. The chase then leads to a diner, where Rennie tells a waitress that a maniac is trying to kill them, but she brushes it off, saying that people are like that in New York. Just then, Jason breaks through the door Rennie and Sean escape.
The diner manager then approaches and gets aggressive toward him, but Jason throws him against the mirror like a rag doll. While some people flee for their lives, Jason then passes by the terrified waitress and continues after Rennie and Sean. Eventually the chase leads to the sewer, where a sanitation worker tells them that at midnight every day (in this case, in 10 minutes) the sewer floods with toxic waste. Before he can show them out, Jason kills him with his own wrench.
Jason then walks up, not noticing Rennie, about to kill Sean with the wrench, but Rennie shines a flashlight in his face, stating ï¿½You didn't get me in the lake, and you're not going to get me now!ï¿½. Jason then chases after her, to which she runs away in fear, trying to hide from him. She then notices a small barrel of toxic waste, opens it with the flashlight, and throws it into Jason's face.
The monster pulls off his mask, showing his scary face melting away (the sludge penetrated through the mask's eye holes and ventilation orifices, thus hitting his face anyway). Rennie and Sean keep running and Jason chases them over to a ladder.
The sewer galleries then flood with toxic waste, dragging Jason away and presumably killing him. Rennie hallucinates that Jason reverts to a child but actually he was washed away into the ocean. Afterward, Rennie and Sean go to explore New York and are reunited with Toby.