“William” is episode sixteen of season nine of The X-Files.
A couple on a farm are waiting for someone to arrive; the wife wonders why anyone would give a child up to strangers. A car approaches and two people get out. The first approaches the couple and the wife asks if the baby is okay. Because why else would the mother give him up? She’s told it was the life choice of a single mother, a terribly difficult decision doe for the good of the child. The other hands the baby over. Meet William.
One week earlier in Georgetown and Scully is arriving home at night. Someone is watching from the shadows.
At the office, Doggett looks at his watch and decides they don’t pay him enough. He heads out. Someone enters the office afterwards and starts looking through the files. In the lift, Doggett realises he’s forgotten something and heads back. When he enters, the intruder hits him from behind. Doggett manages to get up as the intruder runs away, drawing his gun. He tells the other to stop and come forward. As Doggett gets a proper look, his face changes.
Scully arrives at the FBI and meets Reyes in observation. Reyes says the man calls himself Daniel Miller. He’s in a darkened interrogation room with Doggett; Miller wouldn’t speak with the lights on. Scully will understand when she sees him; Miller’s face is severely burned. Fire, maybe acid. He says he’s a victim of what Miller calls the alien conspiracy.
Scully enters the room’ Doggett tells her Miller has refused a lawyer. He got in with a card key he says Mulder gave him. Doggett is going to check his name and address out. Scully speaks to Miller, who says he came to find answers. According to Mulder, the men that did this to Miller are part of a government conspiracy. He says Scully knows who these men are, but he won’t say when he met Mulder. Doggett says some X-files were found on Miller. Mulder’s sister’s abduction. Miller knows about the abduction. Scully says he gives the impression he’s telling the truth or wants them to believe he is. Miller says if he thought he’d be believed, he wouldn’t have snuck in. Scully wants Miller transferred to Quantico to examine his injuries.
As bad as Miller looked, his actual condition is worse, hidden behind facial prostheses and a wig. Scully says the damage wasn’t caused by burning or chemicals. According to Miller, he was injected by something that burned inside and out. Doggett enters; he wants to speak to Scully and Reyes.
Outside, Doggett says that Miller’s identity doesn’t check out. He has a theory though. Doggett doesn’t think Mulder told Miller anything; he thinks Miller is Mulder. Scully doesn’t believe it. Doggett hopes she proves him wrong.
Scully takes a blood sample from Miller. He wants her help to make the conspiracy pay. They did terrible things to her too. Miller says he gave a false name because people at the FBI would kill him if they knew who he was. The same people would kill Mulder. Miller is asking for Scully’s help, but he might be able to help her.
Scully tells Reyes and Doggett the man isn’t Mulder. She’s sure, and they will be after the DNA test. As for now, Miller may be lying but the danger might be real. They will need to figure out what he wants. Get him back to the FBI quietly.
Back at the office, Miller says he didn’t find what he was looking for. The conspiracy to keep the aliens quiet was all but destroyed, but a new conspiracy was formed in the government, of men who are alien themselves. What happened to Miller was a failed attempt. He wants to expose their plans, to do this to everyone. Mulder said there were cases like his, but the files are not here. Someone has already removed them.
The files are at Scully’s. She tells Doggett and Reyes that Mulder and her agreed to bring them here. Mulder would have known where they are. Miller didn’t. He isn’t Mulder. William cries and Miller is standing with him. He wants to hold William. For Mulder.
At no point does Miller claim to be Mulder; in fact, he steadfastly denies he is. Yet he seems to have some of Mulder’s mannerisms and an emotional attachment to William, further confusing the issue. William seems to be in some sort of danger, though.