In Washington, D.C., Scully pushes baby William in his stroller down a sidewalk. She makes her way to an Internet caf�, where she logs on to a server and checks her e-mail. She opens a posting addressed 'Trust No 1.' The message is from Mulder, who speaks of his longing for Scully and William.

Scully�s attention shifts to a young woman, who leaves her baby unattended while arguing with a man on the street. The young woman makes her way back to the Internet caf�, where she apologizes to Scully.

At Quantico, Doggett and Reyes approach Scully with word of an individual contacting the X-Files through intelligence channels who wishes to speak with Mulder because he possesses classified military files on bio-engineered soldiers. But the source will only deal with Mulder personally. But Scully believes it would be a mistake to make contact with Mulder because doing so might endanger him.

As Scully parks her car near her apartment building, she observes the young woman having an argument with a driver. The driver grabs the woman�s baby and speeds off in his car. Scully invites the woman into her apartment, where the woman introduces herself as Patti.

Meanwhile, Doggett summons Reyes to a warehouse. Doggett explains how he successfully traced a phone call from the mysterious source to the building.

A short time later, the young woman�s husband parks in front of the building, exits his vehicle and makes his way inside. The husband speaks with an operative named Shadow Man.

Unbeknownst to Reyes or Doggett, their movements outside the warehouse are being monitored by electronic surveillance. Doggett and Reyes tail the husband from afar. He drives to Scully�s building and makes his way inside. Doggett phones Scully and briefs her on the situation. Scully suddenly grows alarmed. She draws her weapon and confronts Patti, who took baby William out of his crib. Moments later, Doggett observes Patti�s husband attempting to jimmy the lock on Scully�s door. Doggett places the man under arrest.

Patti�s husband explains that he works for the National Security Agency. The couple�s daughter believes there�s something different about their baby, just as there�s something different about William. As Scully�s apartment is secretly wired with surveillance equipment, Patti�s husband witnessed baby William spin a mobile over his crib with the power of his mind. The couple�s baby has performed the same feat. Patti�s husband told his supervisor about his suspicions. According to the supervisor, Mulder is the only person who can put the pieces of the puzzle together.

Moments later, the telephone rings. Scully answers... and speaks with the supervisor, Shadow Man. Shadow Man arranges to meet Scully at the Internet caf� in twenty minutes. The Shadow Man makes Scully take elaborate measures to ensure that she�s alone and not being followed. He makes her drive to a remote location and change clothes. When they meet face-to-face, the Shadow Man threatens to disappear with his information unless Scully makes contact with Mulder.

Doggett tells Scully that the Shadow Man�s demands may be for the purpose of luring Mulder out of hiding so he can be killed. But Scully informs him that Mulder�s return has already been set in motion... and he is arriving by train.

Later, Doggett contacts a forensics technician, Edie Boal, and asks her to examine the change of clothes the Shadow Man gave Scully. Doggett tells Boals he�s looking to identify a man. Agent Boal eventually finds a single gray hair on the clothing and sends it to a lab for analysis. As Mulder�s train approaches the station, Patti�s husband pulls out a gun and appears to aim it at Scully�s head. Reyes alerts Scully.

Scully then sees the Shadow Man at the other end of the platform. He, too, is wielding a gun and pointing it in her direction. Reyes knocks Scully to the ground. It soon becomes apparent that Patti�s husband is aiming at the Shadow Man, not Scully. The Shadow Man opens fire, hitting Patti�s husband. Doggett opens fire, hitting the Shadow Man and knocking him onto the tracks.

The train station manager orders the engineer not to stop at the station because of the shootout. The train continues on its way. Scully can only watch, grief-stricken.

Doggett informs Scully and Reyes that the body of the man he shot cannot be found. The lab results of the hair sample taken from the Shadow Man show that his DNA makeup is part iron, leading Doggett to believe that Shadow Man is also a super soldier.

Scully instructs the station manager to stop Mulder�s train, as she�s convinced Shadow Man boarded it to kill Mulder. The agents receive word that someone jumped off the train and ran toward a nearby rock quarry. Scully and Doggett make their way to the quarry in hopes of locating Mulder. Instead, Scully runs into Shadow Man.

The Shadow Man tells her that either Mulder or baby William must die. Before he can elaborate, his body is suddenly jerked into a red wall of rock, where it disintegrates into a cloud of dust. Later, dust particles at the quarry reform into the Shadow Man�s body.

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