Following the events of the last film, Tommy Jarvis, Thom Mathews is released from the local Hospital for the Criminally Insane. He still suffers from flashbacks of the mass murderer Jason Voorhees, CJ Graham whom he killed several years ago. Tommy returns to Crystal Lake, renamed Forest Green, to confront his fears, along with his friend Allen Hawes, Ron Palillo. The pair visit Jason's grave during a thunderstorm, intending to cremate the killer's body and finally end Tommy's nightmares. After digging up Jason's corpse, Tommy experiences another flashback of his last encounter with Jason. As he impales Jason's body with a metal fence post, two lightning bolts strike the post; this restores Jason as a revenant with superhuman strength.
After killing Hawes, Jason dons a hockey mask (which Tommy has brought). Tommy flees to the sheriff's office, where he attempts to warn the police of Jason's return. The Sheriff Mike Garris, David Kagen, presumes that Tommy is hallucinating Jason's return. On the road, camp counselors Darren, Tony Goldwyn, and Lizbeth, Nancy McLoughlin, get lost looking for Camp Forest Green. They discover Jason, who murders them both.
The following morning, Megan Garris arrives at the station, Jennifer Cooke, along with her friends Sissy, Renée Jones, Cort, Tom Fridley, and Lizbeth's sister Paula, Kerry Noonan. The four teenagers report Darren and Lizbeth missing. Tommy warns them about Jason, who is now considered an urban legend. Despite her prompt attraction to him, Megan is unsure whether to believe Tommy. In the woods, Jason happens upon a corporate paintball game; he crushes the player Burt, Wallace Merck ’s face into a tree, decapitates three other players, and dismembers Roy, Whitney Rydbeck the final player. He also commandeers a machete from the players.
As children arrive at Camp Forest Green, the teen counselors do their best to run the camp. Meanwhile, Garris opts to transfer Tommy out of his jurisdiction to prevent anyone else from hearing his rants about Jason's return. On the way out of town, Tommy makes a run for Jason's grave, which Martin, the caretaker, Bob Larkin has covered up to deny responsibility for the grave being robbed. Hawes' body is buried in Jason's place. A handcuffed Tommy is escorted out of town by Garris, who threatens him if he ever returns.
That night, Jason butchers Martin, along with a nearby couple who happen to witness the murder. Meanwhile, Cort meets with a girl named Nikki, Darcy DeMoss. Jason stalks Cort and Nikki in their RV and lures them outside but the teen couple drives away. Jason pulls Nikki into the RV's bathroom and kills her. Jason then kills Cort, which flips the RV, before Jason walks out. When Garris' men find Nikki's and Cort's bodies, Garris promptly implicates Tommy in the double murder. Garris is convinced that Tommy's "delusions" regarding Jason have driven him berserk.
Tommy contacts Megan for help luring Jason back to Crystal Lake, and she agrees. Meanwhile, Jason makes his way to the camp. He kills both Sissy and Paula but refrains from harming the children. Elsewhere, Garris pulls Tommy and Megan over. She points out that Tommy has been with her for the past few hours; therefore, he could not have killed Cort and Nikki. Nonetheless, Garris locks Tommy up and tells Megan he will decide what to do with her later. Garris and two of his deputies head out for the camp to arrest Tommy's (nonexistent) "accomplice". Jason attacks all three lawmen, forcing Garris to accept that Tommy is right all along.
Jason is about to kill Megan when Tommy calls to him from a boat out on the lake; remembering his killer, Jason goes after Tommy instead. Tommy chains a boulder around Jason's neck, trapping him underwater, but Jason demolishes the boat and drags him beneath the lake's surface. When Megan dives in to rescue Tommy, Jason grabs her leg; she pushes Jason off using the boat's outboard motor, sending him to the bottom of Crystal Lake. Megan swims Tommy back to shore and revives him via CPR. Tommy says that Jason is finally home. The final shot shows Jason underwater, still alive, but powerless to free himself.
