User blog comment:The Milkman/No Love For Leviathan?/@comment-24174486-20120915231103/@comment-24174486-20120916182339

Well, it's not until the ending where you find out what the Crucible is actually capable of. The Citadel and mass relays end up being destroyed in Synthesis, so the destruction of the mass relay could have factored in. (Now that I think about it, the process of Synthesis could have disabled the crew as well.)