The Ending [Reveled][Major Spoilers]

[Zetsumaru]

I think the "kill them all" part is just an enraged Philip due to te death of those he cared (red, howard and the girl) and the treatment he recieved from the hive, running tests on him like he was some kind of lab rat.

You can see how Philip starts as your average guy in overture and slowly turn into his dark and pesimistic side throughout the games, at the end the only thing he could have was revenge, so he took it.

Also wink wink nudge nudge.