On October 31, 1988, Michael Myers is shot and falls down a mine shaft. Sheriff Ben Meeker, the lynch mob of Haddonfield's truckers, and state police toss down dynamite to finish him off. Escaping into a nearby creek before the dynamite explodes, Michael stumbles upon a local hermit and falls into a coma, placing himself in the hermit's care, and being nursed back to health. One year later, on October 30, 1989, Michael awakens, stabs the hermit to death with his knife, and returns to Haddonfield to find his niece Jamie Lloyd again, who narrowly avoided being killed by him the year before.
Jamie has been admitted to the Haddonfield Children's Clinic after having attacked her foster mother. Jamie has been rendered mute due to psychological trauma, suffering from nightmares and seizures and exhibits signs of a telepathic link with her uncle. Dr. Sam Loomis becomes aware of Jamie's psychic link with Michael, and tries to convince Meeker that Michael is still alive. Meanwhile, Michael stabs Jamie's foster sister Rachel to death and begins stalking their friend Tina. Michael kills Tina's boyfriend Mike, then poses as him by wearing a mask that Tina had given to Mike earlier.
Later that night, Tina and her friends Sam and Spitz go to a Halloween party at a farm. Sensing that Tina is in danger, Jamie (having partially regained her ability to speak) goes to warn her. While Sam and Spitz are having sex in the barn, Michael impales Spitz with a rake and decapitates Sam with a scythe. Tina finds the bodies, and goes to warn nearby police deputies but finds that Michael has already killed them. Tina flees, but Jamie and her friend Billy Hill (a fellow patient from the clinic) arrive. Michael begins chasing Jamie but crashes into a tree. Michael exits the car, and Tina sacrifices herself to allow Jamie and Billy time to escape. Loomis arrives, and Jamie finally agrees to help him stop Michael for good.
With Jamie's help, Loomis and Meeker have created a set up at the old Myers house to lure him back to his abandoned childhood home. Suddenly the police receive a call saying Michael has broken into the clinic, which prompts Meeker and most of the officers to leave; however, this call is merely a diversion. Michael appears and kills the trooper sitting in the patrol car outside, before entering the house. Loomis tries to reason with him, but Michael slashes him and throws him over the stair banister. Michael kills another trooper who was protecting Jamie before chasing her throughout the house. Jamie hides in a laundry chute but is forced to abandon it when Michael stabs and injures her. Fleeing upstairs, Jamie find the bodies of Max the dog, Rachel, and Mike in the attic. Michael finds Jamie and attempts to kill her, but stops when Jamie addresses him as 'Uncle," and removes his mask. When Jamie touches his face he goes into a fit of rage, and chases her again. Jamie heads downstairs and finds Loomis. However, Loomis has gone mad and uses her as bait for Michael, luring the killer into a trap and shooting him with a tranquilizer gun. When this doesn't work, Loomis begins beating Michael unconscious with a wooden plank until he eventually suffers from a stroke and collapses on top of Michael.
Meeker and the rest of the police return shortly thereafter and Michael is then taken into custody. Meeker assures Jamie that Michael, who is sitting chained up in a cell, will remain in prison until he dies; Jamie doesn't believe him, however, and remarks that Michael will "never die." One of the officers goes to bring Jamie home when a mysterious man in black, who has been searching for Michael, arrives and causes an explosion at the police station. The officer, hearing gunfire, rushes back inside after warning Jamie to stay with the car. When the officer doesn't return, Jamie goes back inside to investigate and finds the station destroyed from the explosion, along with Meeker and several other dead police officers. Jamie discovers Michael's cell empty and the back door of the police station broken open, causing her to break down in tears as she realizes Michael is free again to continue terrorizing Haddonfield.
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