Assassins creed 2 who is the person at the end

The protagonist is Ezio. The antagonist is "The Spaniard" Rodrigo. Everyone else are Assassin's working with Ezio. After that bit, when you play as Desmond Miles you are fighting the guy from whatever company it is. Desmond was being studied in their labs, when he was "kidnapped" and they are trying to get him back.