I just completed the main quest and am currently doing the Broken Steel quest line, but where does Fawkes go after this? I'd like to pick him up again, I feel naked without him, but I can't seem to locate him. I didn't make him input the code for starting up the generator. I hope he hasn't died in the explosion (or whatever that was at the end), so I ask: did he survive?

On a side note: is the Megaton house know to be glitched? I told Dogmeat to wait inside, exited, came back a day later and he was gone. He's not at Vault 101, even with the 'Puppies!' perk. I hope he's not glitched forever, I don't want to lose my two favourite pals to the games' mysterious inner mechanics

Try going to the Museum of History and look near the door that is the entrance to Underworld.

If you had Fawkes as a follower before you entered the code in the console, he was in the recovery room in the Citadel. Since you did not interact with him there, he should still be there. If not, he should be in the Museum of History.