Good theories so far, though I would add that since Harry can use his suit to hack Peter's, as they're from the same source, I could see Harry using...
Personally, I saw that moment as Magneto sucking the air out of the room from Xavier and laying the seeds to be placed at a spot as close to the top...
'Why?' Just to see the disappointment on your corn-fed, gee-whiz face, Superman. And because a great dark voice on the edge of nothing spoke to me and said you all had to die. There is no 'Why?'