Well, let's remember Primal Earth will still be there - it's just that nobody will be getting in or out. In a brief summary...
The Silver Spartan left Primal Earth at the very last moment, pulled through the dimensional barrier in the middle of the battle against Battallion (note: yes, I have a story excuse for what happened when the mapserver DCd me on top of my machine crashing). Is he coming home? Maybe.
Engine Jean? The lie of being a hero became the truth. The truth of being a villain planning revenge on fellow villains has become the lie and eventually faded. She will never see herself as a true hero - but I know she's still out there, trying to become a better person. And one day, she will go back in time to fight Prothean alongside her younger self. Maybe that time around both of them will get to walk out of it alive.
Ghostslinger? Her task is over. She has earned peace. Until the day the world once again has need of an undead vigilante bound to an ancient spirit of vengeance, she will sleep. Hopefully that will be a very long time.
Booster Angel? She's still out there, in the only world she has ever known, trying to understand what it means to be human. But it will be the character I adapted her from who gets to ask her creators the question: Why?
Captain Freon, whom I've created but never actually got around to playing? He's somewhere on a beach, working on his tan and yet to figure out how this funky suit he found actually works. His story began before CoH, and it is not going to end here.