Mulder, Doggett, and Skinner discover that high-ranking FBI personnel have been transformed into alien "super-soldiers" while Reyes fears for Scully's unborn child as she prepares to deliver the baby on a remote farm.
The episode begins with a metal box being brought in and the coroner examining it. He then notices a small
piece of metal and pulls a piece of metal from the remains of Billy Miles. After the men have left the room, the piece of metal begins to spin, each time, growing into what looks like the beginnings of a spine. Meanwhile, Dana Scully and Monica Reyes pull into the place where Special Agent John Doggett was born in Georgia.
Alex Krycek has been seated in a chair, in Assistant Director Walter Skinner's office, where he is shown a videograph from the morgue, with Skinner telling him that, like shown in the picture, Billy Miles is somehow alive, and is still out to get Scully and her unborn child. Suddenly Agent Gene Crane comes up to Doggett, telling him that there is a person - Knowle Rohrer - who wants to see him, with issues concerning Billy Miles, and Scully. This leaves Fox Mulder and Skinner to interrogate Krycek. Rohrer fabricates a story that Billy Miles is part of some kind Military Project to create a supersoldier. He goes on to say that Scully has been made pregnant using the chip in her neck with the first organic version of that supersoldier. He wants Doggett's help in finding Miles so he can put him down before he finds Scully.
Krycek gets up from his chair in Skinner's office and starts running through the doorway. Skinner chases after him, then turns around and sees Billy Miles behind him. Skinner just manages to escape with Krycek, but Billy
Miles' hand breaks through the elevator, but then slips out. Agent Doggett and Mulder are in the hospital where Skinner is. Mulder distrusts what Doggett has been told by Knowle Rohrer, and the two of them set off to find out how trustworthy Rohrer really is. Reyes has put together an organized and marvelous place for the birth, but as she and Scully stand there, Reyes sees someone running off and follows whoever it is. There, a car pulls up, and she meets a trooper, who agrees to help with the birth. Mulder and Doggett pull into the garage and find Krycek and a passenger, who just happens to be Rohrer, pulling in. Mulder reasons that Rohrer and Krycek are in it together. Doggett pursues Rohrer, where he learns Rohrer has an accomplice: Agent Crane.
Mulder's own problems arise when his phone rings and Krycek disappears from his car. Mulder, having just been told Crane is in on it, reasons that Crane gave Krycek access to the FBI. Suddenly, a hand smashes through the car window and tosses his cell phone on the ground, then Krycek pulls a gun at Mulder, and tells him to get out. Krycek is just about to pull the trigger when a bullet hits him in the arm, and Skinner calmly walks in. Krycek tries to pick up his gun, but Skinner shoots his hand. Krycek pushes his gun over, then tells Skinner to shoot Mulder. Instead, Skinner raises his gun and shoots Krycek in the head. Rohrer and Crane give chase to Doggett, who runs into Skinner. The chase ends up in the parking garage and ends violently with Rohrer running Crane over and then crashing into a wall, causing his car to explode. This allows Doggett and Skinner to escape unharmed.
Scully delivers an apparently normal baby with Reyes and the alien Super
Soldiers surrounding her. Without explanation, the aliens leave the area as Mulder arrives. While Doggett and Reyes report to the FBI Headquarters Doggett places an investigation into Kersh, after a late-night meeting between him and Rohrer. Mulder takes Scully and her newborn baby back to her apartment. After marveling over the baby and discussing recent events, the two agents share a long, tender kiss.
- Scully claims that William is named in memory of Mulder's father, but her own father and brother were also called William (possibly because the baby's last name is Mulder)
- This episode marks the death of Alex Krycek, who is shot and killed by Assistant Director Skinner. Krycek would later return in the series finale, "The Truth", but only as an apparition, hallucination or a figment of Mulder's imagination.
- Several allusions to the story of the birth of Jesus are in this episode including, Mulder following a star to find Scully, and The Lone Gunmen bringing gifts for the baby at the end. Additionally, the super-soldiers having left the birthplace, apparently concluding that who they found wasn't who they were looking for. This parallels the perspective of the Pharisees in the Gospels who refused to acknowledge Jesus as the messiah, having concluded that he was just an ordinary person and not the king they sought.
- This episode is the only time the Cigarette Smoking Man doesn't appear in a finale.
- The opening credits that were introduced in the Season 8 première episode Within make their last appearance.
- David Duchovny as Former Special Agent Fox Mulder
- Gillian Anderson as Special Agent Dana Scully
- Robert Patrick as Special Agent John Doggett
- Nicholas Lea as Alex Krycek
- Annabeth Gish as Special Agent Monica Reyes
- Mitch Pileggi as Assistant Director Walter Skinner
- James Pickens, Jr. as Deputy Director Alvin Kersh
- Kirk B.R. Woller as Agent Gene Crane
- Tom Braidwood as Melvin Frohike
- Dean Haglund as Richard Langly
- Bruce Harwood as John Fitzgerald Byers
- Zachary Ansley as Billy Miles
- Austin Tichenor as Dr. James Langenhahn
- Tom Martin as Pathology Assistant
- Dale Dickey as Game Warden
- Adam Baldwin as Knowle Rohrer