Desmond and some random modern assassins. Alternative universe and stuff. I wish we had a game about modern assassin's brotherhood, but it seems that it's never gonna happen.
I beat Assassin's Creed 3 a couple of weeks ago. Don't want to post any spoilers, but the ending was... WHY, UBISOFT, WHY? I feel sorry for every character who died, like, EVERY. Even the bad ones.
Still, the game was great.