The film takes place after Jason Takes Manhattan. A young woman arrives at Crystal Lake Camp and goes inside one of the cabins to take a quick bath, when suddenly the lights go out. Checking out the problem, she is attacked by Jason Voorhees, who was once again resurrected though never explained how. As the monster chases her into the woods, he soon sees himself ambushed by a FBI special ops team, who riddles him with a hail of bullets before blowing him to pieces with a grenade. The woman is revealed to be federal agent Elizabeth Marcus.
She had been previously assigned to lure Jason out of hiding and into an ambush. His rampage through Manhattan in the previous film had attracted the FBI's attention. As the team celebrates, a mysterious man watches them from the shadows, completely distrustful of their victory. However, they do not notice that Jason's dark heart is "still beating". Jason's brutalized remains are brought to a morgue in Ohio where the coroner, Phil, is hypnotized by Jason's still-beating heart into eating it, allowing Jason's spirit to take control of Phil.
The coroner's assistant makes the poor choice of insulting the serial killer. He murders the assistant with a probe and kills the two FBI agents guarding the autopsy room entrance before escaping. Meanwhile, American Case Files sensationalist newscaster Robert Campbell interviews bounty hunter Creighton Duke, an expert on Jason and the same man who witnessed the FBI's ambush on Jason. Duke explains that Jason will keep resurrecting again and again unless he is killed by a member of his own lineage.
Jason has a half-sister named Diana Kimble, her daughter Jessica and baby Stephanie, Jessica's newborn daughter. After the interview, Duke goes to Joey B.'s Diner, where Diana works, and attempts to tell Diana what he knows, but he is arrested by Sheriff Ed Landis for harassing Diana. Jason, in Phil's body, makes his way back to Camp Crystal Lake, where three teenagers, Alexis, Deborah and Luke, are camping in honor of Jason's supposed demise. After they all go skinny dipping, Deborah and Luke go into the group's tent to have sex.
Alexis stays outside to sleep in a sleeping bag. After peeing on a bush, Alexis is attacked by Jason and is slashed to death with a scalpel. A few seconds later, Deborah goes outside to retrieve a condom (as well as pee), she then returns so she and Luke can have sex. Outside, Jason then retrieves a metal pole and impales Deborah just as she is having an orgasm and splits her in half before killing Luke. He then kidnaps a policeman named Josh after murdering his girlfriend, Edna, and takes him to the old Voorhees house.
After restraining and shaving him, he transplants his soul (in the shape of a black snake-like demon) through his mouth. Jason, now using Josh's body, attacks Diana in her home. Then, Diana is rescued by Steven Freeman - Jessica's former husband and Stephanie's father - who was asked to see Diana earlier. Then, Steven stabs Jason in the back with a fire poker. However, the killer fatally wounds Diana and escapes. Agonizing, she tells Steven to protect Jessica and the baby before it's too late, and dies right after.
Then, Steven is wrongly accused and arrested for Diana's death. In his cell, he meets Duke, who tells him (at the cost of Steven letting Duke break his fingers) the secret on how to kill Jason: the monster can only return to his normal and near-invincible state if he can transplant his soul into one who shares his blood, and that his very blood relatives - like Diana, Jessica and Stephanie - can either resurrect him completely or destroy his demonic heart and kill him permanently. Escaping prison, Steven sets off to get Jessica before Jason can.
Then, Steven proceeds to Joey B's diner, where Diana worked. Then, he saw his daughter for the first time but Ward, one of Diana's work colleagues, appears. At first, Ward doesn't believe in Steven's innocence, but eventually makes amends and lends his car. Then, Steven goes to the old Voorhees house to search for any evidence that may prove his innocence to Jessica. Then, he ends up falling through some floorboards where he discovers that Robert Campbell stole Diana's corpse and hid it in the old house.
Robert Campbell is a newscaster on American Case Files and Jessica's current boyfriend. He intends to "discover" and use the body as "proof" to skyrocket his show's ratings by revealing to the public of Jason's return from the grave (using Diana's "discovered" corpse as evidence). Just then, Jason bursts in and transfers his soul into Robert, leaving his old body to slowly dissolve and die into a bloody puddle. After Jason left, now in Robert's body, Steven makes his way to Jessica, who is taking a bath inside the house, still depressed about her mother.
Steven pursues the murderer, manages to save Jessica, and runs over Jason with Ward's car. Unfortunately, Jessica does not believe Steven despite his pleas and abandons him on the roadside. Later, Steven was arrested by his friend Randy Parker, but eventually allows himself to be taken in when he finds out that Jessica happens to be at the prison. Having recovered from his injuries, Jason goes on a bloody rampage, slaughtering most of the police officers and again is close to possessing Jessica
But Steven arrives and shoots him (even still handcuffed he manages to knock out Officer Randy and grab his gun). Realizing that Steven was telling the truth all along, Jessica follows with Steven to Joey B's diner to get Stephanie. But Joey, the diner's owner, still believes that Steven murdered Diana and threatens to kill them both until she believes that Steven helped Jessica. As Jessica tries to disarm Joey, the gun accidentally fires and the bullet hits the fuse box, causing a total blackout.
Unfortunately, Jason arrives, and makes quick work of Ward outside by snapping his wrist to the point of tearing out most of the bone. Jason forces his way inside and attacks Shelby by dunking his head into the deep-fat fryer, and hits Joey in the jaw hard enough to push the entirety of her jaw into her mouth, killing both. Vikki appears, armed with a shotgun, and manages to shoot Jason multiple times and impale him with a BBQ skewer, but is killed when she's pulled into the skewer and her head is crushed.
After that, Sheriff Ed Landis and Officer Randy arrive at the thrashed diner and Jason transplants his soul from Robert to one of the policemen. It is then revealed through a letter that Duke has Stephanie with him at the Voorhees house and demands Jessica to meet him there alone. Duke had managed to escape the prison earlier when Jason attacked. She goes there and Steven grabs a machete from the wrecked diner. Arriving at the old mansion, Jessica finds Duke. The bounty hunter gives her a magic dagger.
He explains to her that only a Voorhees blood relative like her, Diana or Stephanie, can either resurrect Jason or destroy him permanently. Not long after, Duke falls through some weak floorboards and badly injures his leg. Then, Sheriff Landis and Randy appear, but one of them is revealed to be possessed. Landis accidentally kills himself on the dagger and Jessica drops the blade under a dresser. Randy, who is revealed to be the one possessed by Jason, tries to transplant his soul into Stephanie, but Steven appears and severs his head with his machete.
Jason's heart, which has now grown into a demonic infant, crawls out from Randy's slashed neck and falls to the basement. As Jessica and Steven help Duke to get out of the basement, Jason's heart transplants itself into Diana's corpse. According to Duke, Jason does not need a living member of his family to be revived. Now fully reborn into his original body and complete with his hockey mask, Jason attacks the trio. As Jessica and Steven look for the dagger, Duke handcuffs Jason in an attempt to stall him.
Jason grabs and kills Duke with a back-breaking bear hug. Enraged, Steven tackles Jason and sends them both out of a window where the two engage in a battle to the death with Jason constantly gaining the upper hand. Just as Jason is about to kill Steven, Jessica jumps onto the monster's back and stabs his heart with the magic dagger from behind. As Jason weakens, Steven punches his face and Jessica drives the dagger even further into Jason's heart with a powerful kick.
From the monster's open wound, balls of energy come out as demonic hands burst out from the ground and begin dragging Jason underground. Though the killer tries to drag Steven down with him, Jessica pulls him free as Jason is dragged down into hell forever. They both kiss and walk off into the sunrise with their daughter. A dog finds and tries to unearth Jason's discarded mask, and a passing wind blows away the dirt, when Freddy Krueger's clawed hand suddenly emerges from the ground and drags the mask down into Hell with an evil laugh at the background.