Luckily, with incursions there is a handy middle ground! Every time another Earth is incoming, the Illuminati are alerted with an 8(? maybe? 12?) hour countdown. So maybe the incursions have been happening all along (or since I...petered out, so Tony disappeared for long lengths of time), and with this latest countdown they're officially out of options so Tony comes out like 'okay we have to evacuate the whole planet in this many hours' and really quickly tried to explain. In the meantime, he's prepared for that because that's who he is and is like 'go to all of these evacuation points, there's ships waiting' So that's fucking chaos because you can't evacuate city that fast, so we can play that part out and the reasons why certain things happen later depending on what you want to do with your characters.
And then, again because Tony would plan for these things, the ships are all controlled by Jocasta or something and are supposed to like meet up in orbit and Power Ranger together into a supership that is either like a habitable planet on its own, or use their powers combined to terraform a planet Tony already picked out or something control freak crazy, but then Jocasta goes Ultron nuts and everyone is scattered instead, fighting against their own ships and dealing with SPACE.