Plot summary
Dana Scully (Gillian Anderson) is at a coffee shop, where she replies to an email from Fox Mulder. Later, she is visited by John Doggett (Robert Patrick) and Monica Reyes (Annabeth Gish), who inform her that they have a tipster who claims to have vital information about the Super Soldiers, but he will only talk to Fox Mulder. Scully lies that she cannot contact Mulder, fearing for his safety.
Scully offers support to Patti, another young mother, who spends the night at her apartment. The following day Patti's husband attempts to break in, pursued by Doggett and Reyes. He reveals that he works for the NSA and has discovered the Super Soldier project and wants to expose it to Mulder. He says that their daughter is also a special child like William and that they are trying to protect them. Scully is then phoned by the NSA agent's boss, the Shadow Man (Terry O'Quinn), who provides her with instructions to meet him at a remote location. There, the Shadow Man confronts her, saying that he knows everything about her, including "that one lonely night you invited Mulder to your bed." He then tells Scully that he has information on the Super Soldier project, but he will only surrender it to Mulder.
Scully contacts Mulder to tell him to come back by train, hoping to get the information from the Shadow Man. Doggett warns her that it might be a trap, but Scully is determined to see Mulder again. They go to the train station with Reyes and the NSA agent, but the Shadow Man shows up and kills the agent. He then tries to shoot Scully, but Doggett saves her by shooting the Shadow Man, who falls under the train and disappears, confirming to Doggett that he is a Super Soldier.
Due to the shootings the train passes by without stopping, and the agents learn that someone jumped off it near a rock quarry. They travel there to search for Mulder, and Doggett and Reyes see a figure fleeing in the distance. Scully encounters the Shadow Man, but he is suddenly destroyed by the magnetite in the quarry. Scully continues to email Mulder, but no longer expects him to reply.
Credits
Adapted from Wikipedia contributors, Trust No 1. Paragraphs and formatting adjusted; illustrations, reference markers, block quotations and non-story material omitted.