The undead serial killer Jason Voorhees, thought to be killed in Part 8, is back at Crystal Lake. As he is about to kill a woman the FBI springs a trap. After gunning him down they blow him to pieces. His remains are sent to a morgue, where the coroner becomes possessed by the demonic spirit of Jason. Jason, now in a new body, begins to kill again.
Jason then goes to Crystal Lake, where he finds three partying teens. While two of them have sex, Jason kills the third. He then kills the other two. Jason then attacks two police officers, killing one and possessing the other.
Meanwhile, bounty hunter Creighton Duke finds out that only members of Jason’s bloodline can truly kill him and he will return to life if he possesses a member of his family. The only living relatives of Jason are his half-sister Diana Kimble, her daughter Jessica, and Stephanie, the infant daughter of Jessica and Steven Freeman.
Jason makes his way to Diana’s house. Steven bursts in and attacks Jason. Diana is killed and Jason escapes. Steven is falsely accused and arrested for Diana’s murder, and meets Duke, who reveals Jessica’s relation to Jason. Determined to get to Jessica before Jason does, Steven escapes from jail.
Jessica is dating an American Casefiles reporter. Steven goes to the Voorhees house to find evidence to convince Jessica, but falls through rotten boards. Robert enters the upstairs room and receives a phone call which reveals that he is attempting to “spice up” his show’s ratings by putting emphasis on Jason’s return from death, having stolen Diana’s body from the morgue for this reason. Jason bursts in and transfers his heart into Robert, while Josh melts. Jason leaves with Steven in pursuit. Jason attempts to be reborn through Jessica but is disrupted by Steven who hits him and takes Jessica into his car. Steven runs over Jason, explains the situation to Jessica who disbelieves him and throws him out of the car. Jessica goes to the police station.
Jason arrives at the police station and kills most of the officers. He then nearly possesses Jessica before Steven stops him; Jessica realizes Steven is right. In the chaos, Duke makes his escape. Jessica and Steven make their way to the diner to grab the baby. Jason arrives but is attacked by the owners of the shop. He kills the owners, but is injured by an attacker whom he kills. Jason is presumably killed, and Jessica and Steven discover a note from Duke, telling them that he has the baby and demands that Jessica meet him at the Voorhees house alone.
Jessica meets Duke at the Voorhees house and is given a mystical dagger which she can use to permanently kill Jason. Meanwhile, a police officer enters the diner where Robert (possessed) transfers his heart into him. Duke falls through the floor, and Jessica is confronted by Landis and Randy. Landis is killed accidentally with the dagger, and Jessica drops the dagger. Randy (possessed) attempts to be reborn through Stephanie, but Steven arrives and severs his neck with a machete. Jason’s heart, which has now grown into a demonic infant, crawls out of Randy’s neck and makes its way to the basement where it crawls into Diana’s dead body. Steven and Jessica pull Duke out of the basement as Jason is reborn.
While Steven and Jessica attempt to retrieve the dagger, Duke distracts Jason and is killed. Jason turns his attention to Jessica and Steven tackles Jason, who both fight outside while Jessica retrieves the dagger. Jessica stabs Jason in the chest, releasing the souls Jason accumulated over time. Demonic hands burst out of the ground and pull Jason into the depths of Hell.
Steven and Jessica reconcile and walk off into the sunrise with their baby. However, after a dog unearths Jason’s mask, the clawed hand of Freddy Krueger appears and drags the mask down to Hell, setting up the events of Freddy vs. Jason.