Deus Ex: Human Revolution is a prequel to the game I am talking about. Deus Ex is one of my all time favorite games, especially for its dark atmosphere and magnificent narrative. I first played it in 2003 and till this date, I find something in it I had never seen before. There are so many ways you can do a mission. Its replay value is immense.
As for the level you left playing the game, that's the only part of this game I didn't like i.e. boss fights. Throughout the game you can sneak past your enemies or knock them out without killing except the boss fights. The one you faced was the first of all (Barrett). It's actually pretty easy to kill him. Take cover when he is firing, run when he is throwing grenades and in between shoot or throw grenades at him. He has a pause time between firing because his hand mounted mini gun takes some time before it fires. Do not try to get to close for a take-down because he'll get hold of you.
If you can, give this whole game franchise a try; it's amazing! I can't talk it up enough!