Lolol. Me too!! I was reading this in another site and they stopped updating for more than a year. And now...I don't know who's good and who's not. For all I know, veronica is the bad guy in the end.
SPOILERS FOR THOSE THAT HAVEN'T ACTUALLY READ ANY OF IT.... Those who have, should be safe, and if I missed anything or made a mistake, please correct me. Just a bare basic synopsis.
I think the bad guys are Bart's real older brothers, and it has been implied that Glen's real older brother's (since we now know Bart and Glen aren't really half-brothers after all), are also somewhere and may be pulling the strings. But no definitive answers yet.
The head priest in the present (he wasn't head in the past) knew about the attack beforehand, so he MAY have been a bad guy then, but doesn't remember enough to know for sure. Everyone else where either used/tools or caught in the crossfire it seems at this point. Again, no definitive answer yet to say for sure.
Here is a link to the wikia of the manga: http://bokuranokiseki.wikia.com/wiki/Bokura_no_Kiseki_Wiki
Hope this helps
I already forgot why the story line and also the characters.. I only remember that a girl reincarnated as a boy and the whole school is full of reincarnated people. (￣∇￣")