The agents catch a horrifically scarred man breaking into the X-Files office... a man Doggett believes is Fox Mulder.
At a remote farm house, a husband and wife eager to adopt meet with two social workers. The social workers introduce the couple to their new son: Baby William. Outside Scully�s apartment, a figure with rasping breath (The Breather) watches from afar as Scully carries William into the apartment building.
Later, at the Bureau, Agent Doggett enters the darkened X-Files office, encountering The Breather. Doggett grabs his gun and orders the mysterious man to put his hands up. The Breather complies - and for the first time we get a look at his disfigured face.
Scully is called to the office, where Doggett briefs her on the case. The Breather claims his name is Daniel Miller, and that he gained access to the building by using an access card Mulder gave to him. He also says he�s searching for answers about his disfigurement, which he blames on the government�s secret research.
It becomes apparent that The Breather is intimately familiar with Mulder�s life. He tells Scully that his scars are the result of being injected with an unknown substance. Meanwhile, Doggett has been unable to verify the man�s identity and begins to suspect that he may in fact be Mulder. Scully refuses to believe this, and tells The Breather that the FBI knows his name isn�t Daniel Miller. He confirms this is true - but refuses to divulge his real name. Scully runs a DNA test.
Later, The Breather claims his scars are the result of the government�s failed attempt to turn him into an alien. He then tells the agents the files he was looking for were not in the X-Files office, and Scully admits that she removed them. Mulder knew this, casting doubt on Doggett�s theory
Scully, Reyes and The Breather make their way to Scully�s apartment, where Scully lets him hold her baby. Doggett shows up with results from the DNA test proving that The Breather is Mulder, but Scully refuses to believe.
The Breather sneaks into William's room and injects him with an unknown liquid. Later, Scully discovers a little blood on William�s sheets and rushes him to a hospital, but doctors cannot find anything out of the ordinary.
Scully confronts The Breather, who reveals that he is Mulder�s half-brother, Jeffrey Spender. He then explains that he injected William with a metallic liquid that turned off his alien qualities. As William is the one thing the aliens need, Spender achieved revenge against his father by transforming the child into a normal human being. He warns that as long as the aliens know where William lives, he will never be safe.
The scene returns to that of the opening. The husband hangs a hand-carved mobile over the baby�s crib. After he leaves the room, William reaches up... but the mobile does not spin on its own.
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