I'm going off of absolutely nothing here but I've gotta think it was Phi. Obviously Sigma and Phi's relationship are the focal point of this game and Phi knows a lot more than she's letting on, given how she also knows how to jump between alternate universes/timelines too. she could know almost everything that's going to take place, and post-escape from whereever the fuck they are, detonate the explosives.
but my memory is too poor to remember who and where everyone was at which times. I assume it couldn't have been Alice and Quark since they're infected with Radical-6 at the time of the second and last bomb finding. but who fucking knows. I have like 5 days off and I'm gonna pound em out.
i assume there are blatant hints that I'm passing by as normal occurrences (like Akane getting fevers) but I haven't picked them out