Six years after the events of Halloween 5, the "Man in Black" seen throughout the previous story has rescued Michael from the Haddonfield Police Station and abducted his niece Jamie Lloyd Jamie, now fifteen, has been impregnated and her baby is born on October 30, 1995. The baby is carried away by the Man in Black who appears to be the leader of a Druid-like cult. Later that night, Mary ), a nurse, helps Jamie escape with her baby whom she warns is in harm's way. Michael in pursuit of Jamie and her newborn, kills the nurse. Jamie and the baby flee in the stolen pickup of a drunk motorist (who quickly becomes Michael's next victim) and hides at a dark and deserted bus station.
Meanwhile Dr. Loomis
), now retired, is visited by Dr. Terence Wynn who appeared briefly in the first story and now the chief administrator of Smith's Grove Sanitarium, who wants him to return. During their conversation they overhear Jamie's plea for help on the radio after calling into a local radio station, only to be ignored by DJ Barry Simms ), who is doing a broadcast on the Haddonfield murders. Jamie escapes only to later be run off the road by Michael. Beaten and exhausted, she makes her way inside of an old barn where Michael kills her by pushing her onto a corn thresher. However, Michael finds that Jamie's baby is not in the truck.
Back in Haddonfield, Tommy Doyle the child Laurie Strode babysat in the first storynow lives in a boarding house run by a mysterious old woman named Mrs. Blankenship ). The people living in the Myers house across the street are relatives of the Strode family who had adopted Laurie: Kara Strode), her six-year-old son, Danny her teenage brother, Tim and her parents Debra and John For years, Tommy has been obsessed with finding the truth behind the murderous motives of Michael Myers. After hearing Jamie begging for help on a local radio show as well, Tommy finds her baby at the bus station, takes him into his care and names him Steven. Tommy runs into Dr. Loomis at the Haddonfield Memorial Hospital and tells him of the Strodes living in the Myers house. The two are convinced Michael has indeed come back to Haddonfield.
While the children are at school, Dr. Loomis visits Debra and reveals to her that she is living in Michael's home. After he leaves, Debra calls John to tell him she wants to leave Haddonfield but is then killed by Michael. Later, Kara returns home to find Danny in his room with Tommy, whom he had met while on his way home. The three of them go to Tommy's house across the street, where Tommy reveals to Kara that he believes Michael is under the curse of Thorn by the Druid cult. Thorn is an ancient Druid symbol that represented a demon that spread sickness and caused destruction. To prevent this, a child from each tribe was chosen to inherit the curse of Thorn to offer a blood sacrifice of its next of kin on the night of Samhain (Halloween). When the corresponding Thorn constellation appears, Michael appears. The curse explains why Michael is out to kill his family and also accounts for his superhuman abilities. Tommy believes that baby Steven will be Michael's final sacrifice.
While Tommy goes out to look for Dr. Loomis at a party at the Haddonfield Junior College, Mrs. Blankenship reveals to Kara (after talking to Danny) that she was babysitting Michael Myers when he killed his sister many years ago, and that Danny hears the "voice" (from the "Man in Black") telling him to kill just like Michael did when she was babysitting him the night he killed Judith. Thus, Danny will be the next child cursed by Thorn after Steven's sacrifice. Meanwhile, Michael kills Barry Simms, Tim and his girlfriend Beth After Tommy returns to the boarding house with Dr. Loomis, the "Man in Black" finally reveals himself to be none other than Dr. Wynn. After a terrifying showdown, the "Cult of Thorn" takes Kara, Danny, Steven, and Michael to Smith's Grove Sanitarium, with Tommy and Dr. Loomis drugged for the time being. When they awake, they follow the cult to Smith's Grove where Loomis confronts Dr. Wynn. Wynn credits him for first recognizing the evil the cult has inflicted inside Michael, and indicates how Jamie's baby represents a new cycle of it. After inviting Loomis to join in on his conspiracy, Loomis calls Wynn out on his evil scheme before being knocked unconscious by cult members.
Meanwhile, Tommy finds Kara locked in a room in the maximum security ward. After a brief confrontation with Michael, they continue on to find Danny and Steven. In the hallway they see Wynn and a team of surgeons dressed in cult robes walk into an operating room to perform a mysterious procedure. Tommy and Kara soon sneak into the adjoining room where they find the children. They watch the doctors begin to perform the procedure, but Michael, angry at being exploited, interrupts it, walking in with a surgical machete and slaughtering them all (though Wynn's fate appears to be ambiguous). Tommy, Kara, and the kids run with Michael in hot pursuit until they hide in a high-tech medical laboratory. Inside the lab, Kara notices tanks containing human fetuses with a chart of runes and scientific letter codes; both connected together by the Thorn symbol.
Michael breaks into the room where Tommy injects him with tranquilizers of a corrosive and beats him into unconsciousness with a lead pipe. As Dr. Loomis, Tommy, Kara, Danny, and Steven are about to escape, Loomis tells them to go on without him because he has "a little business" to attend to. Back inside the building, Michael's mask is found lying on the floor of the lab room as the screams of Dr. Loomis can be heard in the background.
