The remains of Billy Miles are brought to a morgue; not long after, Miles walks out again after a single metallic vertebra begins replicating to reconstruct him. Reyes takes Scully to Democrat Hot Springs, an abandoned resort in Georgia where Doggett was born, and the two make preparations to have her baby. Rohrer, who works in the intelligence community, tells Doggett that Miles is the result of a military experiment to create a super-soldier, and Scully's abduction and subsequent pregnancy are a result of an effort to create an organic version of one. Rohrer also says the military/intelligence/whatever conspirators intend to put Miles down. Skinner is nearly killed when Miles returns to the FBI building, allowing Krycek to escape his custody.
Mulder and Doggett watch Krycek arrive at the FBI parking garage, a passenger in a car driven by Rohrer. Miles shows up at Democrat Hot Springs and attacks Reyes, then is shot and apparently killed by a game warden who has agreed to help the agents. Doggett follows Rohrer into the building and sees him meet up with Crane. Mulder realizes that they've discovered where Scully is and gets Doggett to tell him her location. Krycek confronts Mulder and says he's been trying to stop the colonization and Mulder's just been getting in the way. He seems about ready to kill Mulder when he is shot by Skinner. Krycek tries to get Skinner to kill Mulder, but Skinner executes him instead.
Scully starts to go into labor, and Reyes sees that the game warden is a super-soldier. Reyes attacks the warden with boiling water, but can only watch as Miles revives and other super-soldiers arrive. Crane and Rohrer go after Skinner and Doggett, but both are apparently killed in an ensuing car chase in the parking garage. The super-soldiers don't interfere as Scully gives birth to a healthy baby boy, and Mulder arrives in a helicopter as they leave. Kersh is angry with Doggett and Reyes for the whole incident, but neither one backs down; they also note how the bodies of Crane and Rohrer were never found. Mulder and Scully wonder why the super-soldiers didn't take the child (whom Scully has named William, after Mulder's father). Mulder suggests that he didn't turn out to be what they expected, but that he's still a miracle. And then Mulder and Scully kiss.
Dale Dickey, who plays a game warden, also played Patty the Daytime Hooker on My Name is Earl.
Episode Body Count
Alex Krycek: shot by Skinner in the parking garage of the FBI building.
Reyes says that Agent Gene Crane and Knowle Rohrer were both presumed dead but went missing, so you can add vehicular trauma to the list of things that doesn't kill a super-soldier.
Billy Miles: reconstructed from a metallic vertebra found in the remains of his body. Sort-of killed again when a game warden shoots him with a shotgun, but he recovers from that as well.
Season Body Count
Everything increases, especially humans.
Cumulative Body Count (182/202 episodes, 1/2 movies)
Humans: 2,103Creatures: 129
Grand Total: 2,296