23rd Oct: It's time for the Second TV Tropes Halloween Avatar Contest! Details here.
The FreakAngels broke the world via...They were shown causing earthquakes, freak weather, and breaking the Earth's magnetic field. This would probably cause a worldwide EMP, so any electronic device in use at the time, including every power plant in existence, broke at once. They may have also affected the moon, causing freak tides and thus worldwide flooding.
The American military is the real Big Bad.Throughout Mark's return, it's been hinted at he's seen something that the Freakangels should be afraid of. His whole purpose in returning was to protect himself from this threat, a threat which ultimately results in him getting a stroke in two weeks that he will not break out of. Then the last panel here indicates the problem. The fact that a functioning American military helicopter survived the Freakangels apocalypse, plus the tendencies of militaries in post-apocalyptic settings, make for the obvious conclusion.