TRUST NO ONE

While at a coffee shop, Dana Scully (Gillian Anderson) sees an infant crying and sees its mother, Patti, arguing with her husband outside. Scully asks the mother if she is okay, and the mother leaves with her child. Meanwhile, John Doggett (Robert Patrick) and Monica Reyes (Annabeth Gish) visit Scully at Quantico to tell her about a tipster who wants to contact Fox Mulder (David Duchovny). Doggett encourages Scully to contact Mulder, believing the tipster has the names of the Super Soldiers and could prove vital to tracking them down. The tipster indicates that he is willing to share this information with no one other than Mulder. Scully, fearful for Mulder's safety, falsely claims not to know his whereabouts.

A short time later, Scully sees Patti having another argument with her husband, who drives off with their baby in the car. Scully approaches Patti, offering her assistance. Scully convinces Patti to stay over that night in her apartment after learning she has nowhere else to go. Meanwhile, Doggett and Reyes stake out the location where he traced the tipster's call. They see Patti's husband, who they believe to be the tipster, walk inside the apparently abandoned building. Inside, the husband sits at a computer. The Shadow Man (Terry O'Quinn), who appears to be the husband's boss, monitors Scully through surveillance.

The next morning, Patti shuts off the baby monitor and removes William from his crib. Scully awakens when she gets a phone call from Doggett warning her that the tipster they were following had just gone into her apartment building. Scully then hears William cry and confronts Patti at gunpoint. Just then, Patti's husband attempts to pick Scully's lock, but is stopped by Doggett and Reyes. The husband informs the agents that they are being watched, and signals to Scully to close the window. He then reveals to Scully that he is an NSA employee with no name. Patti says their daughter is just like William, and they only want to keep both children safe. The husband reveals that his supervisor has discovered the “Super Soldier” project and alludes to crimes against innocent people. He begs Scully to call Mulder out of hiding in order to give him this information.

Moments later, the Shadow Man calls Scully and tells her that she contact get Mulder in one day or else he will disappear with the Super Soldiers' identities. Scully refuses unless she can meet with the Shadow Man face-to-face. The Shadow Man gives Scully detailed instructions about how and where to meet him, warning her that even a slight deviation from his instructions would mean that he will never contact her again. The Shadow Man tells Scully to drive west in a series of vehicles until she is told to stop. He also tells her to change into a different outfit that he has in the trunk of the car she is driving; Scully reluctantly complies. The Shadow Man then comes face-to-face with Scully and destroys her vehicle with a remotely detonated bomb. He explains that he has been watching her for quite some time, and that, in addition to her clothing size, he knows everything about her, including "that one lonely night you invited Mulder to your bed."

Scully finally gives in and contacts Mulder; she tells Doggett that before Mulder left, they had worked out a plan that, if he was to return, he would be arriving by train. Doggett urges Scully to contact Mulder and tell him not to come, fearing that the Shadow Man is setting a trap for him. Scully replies that she wants to see Mulder, and that it is too late to call it off. Reyes, Doggett, and the NSA agent cover Scully at the train station. However, as the train pulls up, the Shadow Man appears and guns down the agent before approaching Scully. Before the Shadow Man can kill Scully, Doggett appears and shoots him twice, sending him falling onto the train tracks, where the train seemingly runs over him. Because there has been a shooting, much to Scully's dismay, a train employee radios to the conductor to keep the train moving and not to stop at that station.

While Scully consoles Patti, whose husband just died in Scully's arms, Doggett reports that he cannot find the Shadow Man's body. Scully, fearful that he is a Super Soldier pursuing Mulder, chases after the train with Doggett and Reyes. An employee who works for the train gets a call on his radio, saying that someone jumped off a train and into a rock quarry. Doggett and Reyes chase after someone they believe to be Mulder, while Scully goes deeper into the quarry. There, she is attacked by the Shadow Man. Suddenly, the Shadow Man is destroyed by the magnetite being mined from the quarry

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