Scully gets an e-mail from Mulder, who expresses his wish to come home to her. When Doggett tells her that someone is willing to leak the names of the super-soldiers to Mulder, however, she says she doesn't know how to contact him. Doggett doesn't believe her, and says the information will allow Mulder to come home, but she thinks it will compromise his safety. Doggett and Reyes manage to track the source to his building, which we see includes a big surveillance operation. Scully takes in a woman named Patti, who appears to be having marital difficulties, but is actually in league with the source. The agents expose them as the source, an NSA man, tries to break into Scully's apartment.
The NSA man and Patti say their daughter has also shown signs of supernatural powers like William, and they feel that Mulder is the only one who can connect all the dots about that and the super-soldiers. Scully gets a call from a shadowy guy who works with the NSA man; using a distorted voice, the Shadow Man directs her to an isolated location to meet. He says he knows everything about Scully's life, and that he needs to reach Mulder for the good of humanity. Doggett is second-guessing the meeting, but by the time he sees Scully again she's already called Mulder back via train.
Scully and Reyes wait for him at the train station, as the NSA man arrives and spray-paints over the surveillance cameras. The train arrives, the Shadow Man shows up and kills the NSA man, and Doggett shoots the Shadow Man, who falls onto the tracks. Due to the melee, the station manager orders the train to keep moving, despite Scully's protests. The Shadow Man isn't found, and that coupled with an FBI analysis of some clothing he gave Scully makes Doggett realize that the Shadow Man is a super-soldier who managed to board the train. Both Mulder and the Shadow Man jump off the train farther down the tracks, and the agents go to investigate. The Shadow Man confronts Scully, saying either Mulder or her son must die. Then he gets sucked into a band of an iron compound at the quarry, destroying him. Scully sends Mulder another e-mail, vowing to see him again and carry on the fight.
Mrs. Landingham as an FBI agent? Yep, Kathryn Joosten, who played the President's assistant on The West Wing and currently plays Karen McCluskey on Desperate Housewives, plays Agent Edie Boal here. And my Lost addiction requires me to mention Terry O'Quinn appears in this episode as well as the Shadow Man.
Episode Body Count
Cadaver: Scully uses a dead body in one of her classes; it seems like there may have been a separate one for an earlier class, but that's not certain.
Man on the Street: on the left there. An NSA guy, dies after being shot by the Shadow Man at the train station.
Shadow Man: destroyed after exposure to some sort of iron compound at a quarry.
Cumulative Body Count (188/202 episodes, 1/2 movies)
Humans: 2,132Creatures: 130
Grand Total: 2,326