[SPOILER] Penumbra - finally finished :) - thoughts on the game series...

[Desperate4God]

I'm pretty sure that it is implied that Philip died or became infected. At the end of Black Plague, he is knocked unconscious or killed, and Requiem supposedly takes place in his mind. At the end of Requiem, he is given the choice to kill himself (along with Red), or to leave on the ship. The ship, however, is the not the one he arrived in, but rather the one from his delusion or dream when Clarence first took over.