Be prepared to die a few times. Beware of the edge of the room, as you can fall off. Also, do not hide behind the pillars for too long. They will open up and arc electricity periodically. When you walk into the room, a giant bay door at the opposite end of the room will open, revealing the "new and improved" Sarge. As soon as that door opens a crack, start lobbing rockets in there. After you score about six good hits without being splattered by his BFG, break out the Soul Cube (that you should have charged before entering the room) and let him have it. It should kill him and heal you. Pick up the armor and ammunition around the room before continuing.