In the introduction, William has been given up for adoption to a Wyoming couple. One week earlier, a heavy-breathing man observes Scully coming home with William and later sneaks into the X-Files office, trying unsuccessfully to knock Doggett out. Captured, the man identifies himself as David Miller; he says his body has been heavily scarred after he was given an injection as part of the alien conspiracy, and that he was given a keycard by Mulder to access the building. Doggett finds that the Miller identity doesn't stack up, and proposes that he's actually Mulder...something Scully is reluctant to accept. Not Miller admits that he lied for his own protection, since there are people at the FBI who would kill him if they knew he was there.
Not Miller says he was disfigured as part of a failed attempt to turn him into a super-soldier, and that he was seeking files related to similar cases but they were missing. It turns out that Mulder and Scully agreed to remove the same cases from the X-Files before he went on the run, and she decides to let him see them (and also William, who Not Miller says is part alien). Scully seems to be considering that Not Miller might be Mulder, but is still unwilling to believe it even after the DNA matches.
After unsuccessfully trying to escape the agents, Not Miller fakes sleep and gives William an injection. William is taken to a hospital, where it is found that he's OK. Scully realizes that Not Miller is actually Jeffrey Spender, who says that the DNA test is a result of he and Mulder both being fathered by Cancer Man. Spender also says he injected William with a form of magnetite, apparently removing the alien part of his biology, as revenge on Cancer Man, but warns that William will still be in danger of those seeking to use him for the alien colonization. Reluctantly, Scully gives him up for adoption to protect him.
Directed by David Duchovny, who also had a role in the story.
Episode Body Count
Jeffrey Spender: not killed by his father after all, but rather subjected to a horribly botched attempt to turn him into a super-soldier.
Cumulative Body Count (198/202 episodes, 1/2 movies)
Humans: 2,209Creatures: 131
Grand Total: 2,404