Sam Gideon was thought to be dead. Killed in the explosion of the Providence colony after defeating Victor Zaitsev, the leader of the Order of the Russian Star. That's what everyone thought anyway...
So yeah, this is a Vanquish/MLP mix. If you haven't played Vanquish, I suggest you go and pick it up. It's very cheap these days and is an amazing third person sci fi shooter. If you're into third person shooters, you'll love it. Anyway, enjoy!