The Smoking Man
In the season 11 finale "My Struggle IV", the Smoking Man and Reyes follow Mulder, Scully and Skinner to an abandoned factory where they are chasing down William. Skinner points a gun at them and shoots Reyes dead, and the Smoking Man runs Skinner over in his car. The Smoking Man confronts "Mulder" (who is actually William in disguise) by a waterfront, and during the standoff shoots him in the head and causes him to fall into the water. The real Mulder appears and shoots the Smoking Man, who realizes that he has killed William, and he falls off the edge and into the water, with his body then carried away by the current.