MULDER PURSUES AN ALIEN TRYING TO RETURN TO ITS SHIP, WHILE SCULLY INVESTIGATES THE SHOOTING OF ASSISTANT DIRECTOR SKINNER.
Assistant Director Walter Skinner warns Scully as he is wheeled into surgery that he recognized the man who shot him. Although the Bureau is ready to write the incident off as a random shooting, Scully presses the investigation and discovers that the man who shot Skinner, Luis Cardinal, is the same one who shot her sister. Mulder, meanwhile, is unknowingly escorting an alien life form into the United States, one which is "hiding" inside Alex Krycek. When the pair is run off the road into a ditch by agents of the Cigarette-Smoking Man, Mulder is too dazed to see Krycek kill their assailants by irradiation. Although Krycek flees, Mulder still has the key to Krycek's locker. With the aid of the Lone Gunmen, he recovers--an empty digital tape box. But he discovers a phone number on the package: the phone number of the Well-Manicured Man. Scully meanwhile fears for Skinner's life; she foils an attempt on his life by Luis Cardinal. Mulder, meanwhile, has learned that the cargo salvaged from the sea floor by the "Piper Maru" is being stored in a missile silo in North Dakota; he and Scully arrive and find dead, irradiated soldiers. Knowing Krycek (and the alien inside him) is in the silo, they stalk him through the darkened halls, but are ambushed by the Cigarette-Smoking Man's agents and hustled away. As they are driven off, Krycek kneels on top of a UFO, the alien entity pouring from his eyes and mouth, re-entering its craft. Krycek, still alive, beats on the locked doors in terror, begging to be released.