Phil didn't die in the attack on the helicarrier, which Clint finds out pretty soon (not the rest of the team though, I think). He hides in the ceiling above Phil's bed (pretty much living there) and doesn't eat or sleep enough.
He comes out after some time, I think it was to calm Phil down as the medical personnel was upsetting him. Clint collapses into a chair and later wakes up in a bed himself with an IV in his arm; Fury may have been involved at some point.
Does somebody know the story? :)