But I seem to recall hat with Magic at one point it was going to be a two-book story, and then the editor basically let Wolverine at it and said one book? So maybe there was stuff that was dropped out hat would've explained more of what was going on.
It was never written in full as two books though - it was pitched as two, with a synopsis as two, but it was written as one when it was commissioned. There were assorted other changes too, course (originally it was just Geordi and maybe Barclay on Challenger with an otherwise totally new crew, for example). So while the story arc had to be compressed for IFM, there was also a lot requested to be added in.