Mass Effect 2 doesn't have one of these, with there being only one main antagonist, Harbinger, who uses the Collector General as a mouthpiece. However, the mercenary groups that team up against Archangel have leaders that fit this mold nicely.
Evil Genius - Phantomnote the only one of the five to try both a sneak attack and a boss fight before his stage even begins. His division in the Neo Arcadian army is also stated as the Intelligence Unit. He could also be considered the second Dragon as well, considering he's the most loyal to Copy X, to the point of trying to take Zero with him.
(Note that these are the game-play dynamics. Story-wise, The Alchemist is the Dragon, and the King is the Sixth Ranger Traitor. That leaves Evil Genius to The Hunter, who also fits the role, just to a lesser extent.)