Howard will be doing his thang and his thang is hugging his cats and sleeping.

Seriously though, I'm presuming that he's still the Command liaison with Nathan Petrelli but I need to doublecheck that. He's not going to be doing a hell of a lot because he's a) rattled by Punishment, b) going to GLaDOS himself during the Rebellion and c) doesn't have much to do. He'll continue spreading information around but that's about all I can do with him.