So, this basically ignored every movie since the original?

Basically. Depending on which cut of Halloween 6 you watch, it goes one of two ways, and either way is a cliffhanger:

a) The doctors at Smith's Grove, who are in the Thorn Cult, have been doing experiments with genetic engineering and in vitro fertilization to harness the evil that is inside Michael, and baby Stephen is the result of that. Thorn, the demon that the cult has been trying to keep at bay through Michael for the past 32 years, finally takes control of him, and makes him slaughter the doctors as Smith's Grove. Tommy Doyle injects Michael with corrosive chemicals, and beats him to supposed death with a lead pipe. As Tommy, Kara and the kids escape, Loomis heads back inside to find Michael gone. Either Loomis is killed off here by Michael, or Loomis screams because Michael has disappeared again.

b) The cult of Thorn gathers in the basement of Smith's Grove for the final sacrifice. Michael has to kill baby Stephen to complete what he started 32 years ago, and then the evil will transfer over to Danny, and his first sacrifice will be Kara. Tommy infiltrates the building, and holds Wynn at knife point to let Kara and the kids go. Michael chases after them, and Tommy uses the runes of light to try to cancel the evil energy inside of Michael. Wynn, however, steps inside the runes of light, and cancels their power. Tommy, Kara and the kids escape, and Loomis heads back inside, only to discover that Michael has swapped clothes with Wynn, and as Wynn supposedly dies, he makes Loomis the new leader of the Cult of Thorn, meaning Loomis has to watch over Michael from now on and protect him.

Halloween: Resurrection, either one, but they both suck:

a) Michael just had a death rattle or something, and died on the coroner's table.

b) Michael gets away, never to be seen again.

How was Halloween 2 not a sequel?

Not basically. Did.