For starters, the opening titles themselves are quite different. The entire original cut was not filled with fast-flashing montages, as Joe Chappelle's final cut was. Dr. Loomis performs the opening voice-over, instead of Tommy Doyle.

The film then flashes back to the finale of HALLOWEEN 5. We see Jamie enter the police station, and watch as Michael is shoved into a van outside. The Man In Black kidnaps her, and leaves the police station in explosive flames.

 Jamie escapes with the baby, and finds her way to the farm. But instead of Michael grinding her up, he simply stabs her and leaves her for dead...but she lives. Jamie ends up in the hospital, where she spends a good deal of the film.

 The next morning, the Strodes are having breakfast. As John slaps Kara, we see Danny look outside the window and see The Shape. Dr. Wynn's voice echoes "Kill for him."

Several of the scenes are longer takes than those seen theatrically. A small, but effective, scene is shown as Kara leaves for school. Her parents watch her through the window, and John disowners her, saying "She's not my daughter anymore."

Kara arrives at school, and walks around campus. We see The Shape watching her.

Meanwhile, Jamie is still in the hospital. She dreams about Michael impregnating her while held in the clutches of the Thorn cult. Sadly, the Man in Black appears in her room, tells her "Your work is finished now, Jamie," and shoots her.

The film continues like the theatrical version, without an exploding head, though...many of the scenes paced differently. The plot remains the same until the Thorn members take Kara prisoner - after which the theatrical ending is totally dropped. At Smith's Grove, they have Kara tied up on an alter, where Michael is to perform his final sacrifice by killing the baby Steven and passing the curse of Thorn onto Danny.

In his office [in a completely different take of the scene], Dr. Wynn explains to Loomis how he protects Michael, and how he must pass on his duties to another...to Dr. Loomis! During the sacrifice, Tommy sneaks in, dressed as a cult member. Kara reveals that the baby is Michael's. Tommy suddenly takes Wynn hostage, which allows Kara, Danny, and the baby to run for it. Trapped in the hospital by bars, Tommy takes out his supply of rune stones and arranges them in a special circle. He cuts himself, and adds his own blood to the circle, hoping to cancel out Michael's evil rune with thorns of goodness. Sure enough, he manages to stop Michael dead in his tracks as Loomis comes to the rescue to free them from the gate.

 As Tommy, Kara, Danny, and the baby drive off to safety, Loomis returns inside. As he unmasks Michael's body, he finds Wynn beneath the mask! As Dr. Wynn utters "it's your game now, Dr. Loomis," the Thorn appears on Dr. Loomis' wrist! Sam screams out in terror as Michael walks away, now dressed as the Man In Black.

The film also features an almost completely different soundtrack. Much of this music can be found on the HALLOWEEN 6 original soundtrack.