I beat the normal game, and can't seem to find Fawkes, continuing on with Broken Steel.

He's supposed to be in the lobby of Museum of History, but besides the funny Aqua-Cura guy and his crowd, there's no one there after multiple visits.

I'm guessing I can use the console to get him to me, but wondering why he didn't show up at the lobby. I hadn't sent him away or told him to wait for me before going in to put in the code at the purifier.

Was he in the Citidale?

If not then he might've fallen through the map.

He should be in the medical room of the Citadel. I had this problem too with Clover. The darkness of the room, what she was wearing, combined with her standing in a corner facing the wall made her very hard to see.