With Scully in a hospital ICU, the FBI hierarchy learns that Mulder is alive. So do the conspirators but the Cigarette Smoking Man continues to argue that Mulder is worth far more to them alive than dead. He points Mulder in the direction of a cure for Scully's cancer but apparently pays a heavy price for doing so. He tells Mulder that the alien conspiracy is real and offers to prove it to him. His proof however doesn't quite satisfy Mulder who appears before the FBI review committee to reveal the identity of the conspirator inside the FBI.
—garykmcd