The main remaining "evil Morlock" is Masque, who has the power of reshaping faces. Like the baby-stealing, this is a very primal horror. That a hard-line separatist like Masque has it - and is willing to use it so pettily - confirms our worst fears about such isolationism. We don't know Masque's story, of course. The Morlocks didn't just come from nowhere - they all had mothers and names, but keeping this obscure makes it hard to understand Masque as a victim of the system, and he becomes the most horrific X-Men villain so far.
But think about it a bit and we can infer a back-story. Masque's power is amazing. We see it used here to restore the woman that Rusty had accidentally burned the face off. He can use it at will, and well, to put it crudely, money > bigotry. Not always, not often enough. But enough that he'd have a fair chance setting up a practice on Harley Street (or whatever the New York equivalent of that is) and getting enormously rich. He's not an idiot, and he's bitterly against integrationism. So, he's tried that, and it backfired spectacularly. Maybe more than once.
In the end, no permanent changes are made, to faces at least. Emma (Rusty's victim from #1) refuses having hers back when she learns it comes at the cost of Rusty's, and she instead plans to teach the Morlocks about the Lord. I hope this fails: the addition of evangelism to the already fractious Morlock society could explode it. During all the action, Skids learns to drop her forcefield in a moment of need. And a rather abrupt last page to the issue indicates her and Rusty want adding to the Chart.