Is Michael the father of Jamie's baby?

In the Producer's Cut but not the Theatrical Cut. In the T-Cut, he's an experiment in Dr. Wynn's attempt of cloning Michael Myers, never directly stated but implied by all the test tube microscopes and the fetus tank we see in the lab room showing experimentation on the "Thorn gene" (which had to have come from Michael) was going on for the past six years. The T-Cut removed any trace of Michael being the father since Jamie's death is changed so she could no longer have the flashback of Michael raping her (though Joe Chappelle oddly still uses clips of the flashback in the opening) before the title sequence.

[deleted]

That's pretty sick, even for a slasher movie.

In the Producer's Cut, yes, and that's what ruins it for me.

Horror_Metal

Yes. Awful plot point.