In a montage of surveillance images, Mulder and Scully are seen throughout the years. They are not only captured on investigations, but during private moments in their homes. More recent surveillance footage shows Scully on the platform of a train station, crying over a slain man’s body.
Scully enters an internet café with William and logs onto a private mail box. Waiting for her is a message from Mulder, who expresses his desire to return home to her and to William. As Scully begins her reply, a woman who has entered the café with a baby leaves to argue with a man outside. Scully goes to the unattended baby, and the woman comes back to reclaim her child. Later, at Quantico, Doggett and Reyes tell Scully that a source has been trying to contact Mulder with information about the Super Soldiers. Unfortunately, the man will talk to no one but Mulder. Scully says that she doesn’t know how to contact him, and Doggett questions why she still refuses to trust him or anybody else.
Later that night, Scully returns home and sees the woman from the internet café on her street. The woman is again fighting with the same Man on the Street, but this time he takes her baby and drives off. Scully approaches the woman, who introduces herself as Patti. Feeling sorry for her, Scully offers to Patti to stay the night. Meanwhile, Doggett and Reyes watch a nondescript building that has been traced to the source that had sought out Mulder. A car pulls up, and the driver heads into the building. It is the Man on the Street who had been fighting with Patti. Inside the building is a room full of surveillance monitors. A Shadow Man at an adjacent monitor asks the Man on the Street about his wife and child. As he exchanges pleasantries, the Shadow Man calmly watches on his monitor as Doggett and Reyes break into the Man on the Street’s car outside.
At 5:41 a.m., the Man on the Street finally leaves the building, and Doggett and Reyes follow him. At Scully’s apartment, Patti rises, turns off the baby monitor and picks up William. Scully’s cell phone vibrates, waking her up. It is Doggett, telling her that he and Reyes have followed a strange man to her building. Suddenly alarmed, Scully pulls her gun on Patti, and orders the woman to put down William. Doggett accosts the Man on the Street before he is about to break into Scully’s apartment. The Man will not reveal anything, only muttering, “They’re watching.” Scully suspects that both the Man and Patti had conned her to get to her son. Scully closes her blinds, and the Man finally divulges that he works for the National Security Agency. He can not be traced. Patti confesses that her daughter, like William, is somehow different. The Man knows that William affected movement of the mobile over his crib. He admits that he has not only been watching Scully, but Doggett and Reyes as well. The Man had told his supervisor about the oddities surrounding both his daughter and William. The supervisor believes that they are related to the Super Soldiers, and the Man had hoped that Mulder could somehow make the connection to find out what their children really are. Suddenly, the Shadow Man from the nondescript building phones Scully. He says that he has been listening to the conversation. As he watches their every movement, he does not tell her that he has cameras inside her apartment. The Shadow Man knows that Scully had sent Mulder an email the previous day. She refuses to give him any information on Mulder unless she can see him personally. He instructs her to come alone to the internet café. Although Doggett protests, Scully leaves William with them to meet her secret contact.
As she waits outside the café, Scully is called by the Shadow Man. He directs her to a green car while he watches her from a camera on the street. She is told to start the car and drive into an alley. Then she gets out, and enters another waiting car. As the Shadow Man watches from a camera inside the second car, she drives onto the highway. At nightfall, the Shadow Man has her stop in the middle of a desolate field. He orders her to leave the car running and open the trunk. She is told to change into the clothes inside the trunk. Suddenly, the Shadow Man appears. He has her put her gun and her old clothes inside the car, which he explodes by remote control. He inspects her watch for microphones. Believing her to be free of bugs, the Shadow Man admits that he knows everything about her -- her blood type, childhood fears, pet peeves, etc. -- and has risked his life to talk to her in order to get to Mulder. He warns her that she must contact Mulder. Then he hands her a set of keys to another waiting car.
At Quantico the next day, Doggett expresses his worries that both Scully and Mulder are in danger. He fears that these men are using her to lure Mulder out in order to kill him. Scully reveals that Mulder is already travelling on a prearranged train, arriving at midnight. She can’t call him off.
At 10:48 p.m., Scully waits on the train platform, as Reyes backs her up from a distance. The Shadow Man is also watching her through a security camera. The Man on the Street walks onto the train platform and sprays black paint on a security camera above. Doggett, meanwhile, brings Scully’s clothes from the car to an FBI lab. He asks the technician to quickly look for any traces of a man’s DNA on the clothes.
Just before the midnight train approaches, the Man on the Street sees Scully. Reyes catches sight of the Man on the Street pulling out a gun. Reyes calls out for Scully’s attention, but the Man is not pointing at Scully. Scully notices the Shadow Man come toward her with a gun from the other side. Although the Man on the Street is aiming at the Shadow Man, the Shadow Man fires first and hits the Man on the Street. Reyes pulls Scully to the ground, and the Shadow Man points his gun at them. Suddenly, Doggett arrives on the platform and shoots the Shadow Man repeatedly, sending his body onto the tracks of the incoming train. Seeing the gunfire, the station manager orders the train to keep moving. Scully begs for it to be stopped, calling out for Mulder as the train quickly passes. The Man on the Street dies at Scully’s feet. She is grief-stricken and unsure she will ever see Mulder again.
Police later scan the tracks, but the Shadow Man’s body has vanished. Patti arrives at the station, asking Scully for forgiveness. They had only sought answers, and her husband was trying to protect Scully from the man he worked for. Scully comforts Patti over the death of her husband. Doggett tells Scully and Reyes that the fabric on the clothes from the car show that the Shadow Man has a DNA that is complexed with iron and can not be tested. This seems to prove that the Shadow Man is a Super Soldier who is unstoppable. Scully fears for Mulder’s life, believing that the Shadow Man jumped on the train after him. The station manager is alerted that a man jumped off the train into a rock quarry. The agents drive to where the jump took place, and Doggett and Reyes walk down into the quarry. They see a man running away, and Doggett, believing it is Mulder, calls out to him. Although Doggett identifies himself, the man runs off. Scully drives deeper into the quarry, and calls out for Mulder. Suddenly, the Shadow Man comes out from the fog and chases her. She runs into the quarry, becoming trapped. With nowhere else to turn, she pulls her gun on the Shadow Man, asking him why he intends to kill them. The Shadow Man says that either Mulder or William must die. Suddenly, the Shadow Man struggles as a force wracks his body. His face becomes contorted, and he is magnetically pulled to the quarry wall, flying past Scully and knocking her down. As his body impacts the red quarry wall, it disintegrates into a cloud of dust. Scully gets up and runs off.
The next day, Scully emails Mulder with hopes that he is still alive and will someday see her again.