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Directed by David Duchovny
Skinner: That doesn't make any sense. Mulder knows those files inside out. Why would he direct him? Why not just tell him?
A mysterious and hideously scarred man (Chris Owens) approaches the agents, claiming to have information about a new alien conspiracy that has replaced the old Syndicate. The possibility is raised that he might actually be Mulder.
- Anti-Hero: What Jeffrey Spender has become since being shot in the head and experimented on. His goal is good and noble, his methods are less so and his motives are selfish.
- Archnemesis Dad: Just when it seemed CSM couldn't get any worse, it is revealed that after shooting his own son in the head failed to kill him, he had Jeffrey subjected to hideous experiments, attempting to turn him into an alien Super Soldier, similar to how he had Jeffrey's own mother Cassandra turned into an alien-human hybrid. Somehow Jeffrey managed to survive this as well and escape, but was terribly burned and disfigured as a result. Jeffrey gets his revenge in kind by sabotaging an important part of the Colonists' plans.
- Body Horror: Horrific torturous experimentation to Spender has rendered him severely disfigured, including burns all over his body, most of his hair missing, no ears, melted flesh fusing over his nose, a big hole where a normal nostril should be, a ruined, twisted mouth and his vocal cords and/or lungs are clearly damaged.
- The Bus Came Back: The unexpected return of Jeffrey Spender.
- Character Title: This episode is named after Scully's baby.
- Continuity Nod: Scully's first scene has her sing "Jeremiah Was a Bullfrog" to William, although the word "Jeremiah" was replaced with her baby's name.
- Depower: Spender gives William an injection that will remove his alien-related powers and make him a normal human child, as an "up yours" to the alien conspiracy.
- The Dog Bites Back: Jeffrey gets his revenge at last for all the evil, abuse and manipulation he and his mother suffered through their lives at CSM's hands.
- Fate Worse than Death: What Jeffrey was subjected to at the hands of The Conspiracy by his own father.
- Give Him a Normal Life: Why Scully gives William up for adoption.
- How We Got Here: The episode opens with a social worker handing William over to his new parents, and then goes back to explain why Scully decided to put him up for adoption.
- Hurting Hero: Jeffrey big time, physically as well as mentally from what he has survived.
- Made of Iron: Somehow Jeffrey impressively survived both being shot in the head at close range and horrific experimentation trying to turn him into a Super Soldier.
- Manipulative Bastard: Downplayed in that his end goal was noble and good, but Jeffrey manipulates Scully's feelings about Mulder and the other heroes sympathy to accomplish his objective. Even going so far as to subtly pretend to be Mulder, adopting a couple of his mannerisms. He learned a little bit from his hated father after all.
- Manly Tears: Jeffrey freely sheds them while holding his nephew William.
- Myth Arc: Deals with Scully trying to protect her child and ultimately putting him up for adoption for his own protection.
- Papa Wolf: When Doggett finds out Spender injected William with something he nearly goes full Jack Bauer Interrogation Technique on him, threatening to kill him if anything happened to the baby.
- The Power of Hate: Despite all the agony he was put through, Jeffrey doesn't regret not being killed by the shot to the head, and believes his hatred for his father is the only reason he survived what he did, that only it could never be destroyed.
- Put on a Bus: Scully's baby William.
- "The Reason You Suck" Speech: Scully delivers a scathing one to Spender when she figures him out, one that he doesn't disagree with.Scully: I've seen my share of the hideous, of the disgusting and the repellent... but you sir are the most perfect expression I will ever see of all that is vile and hateful in life.
- This Cannot Be!: Skinner is shocked by his realization of the burned man's true identity.
- Riddle for the Ages: How the hell did Jeffrey manage to escape from the clutches of The Conspiracy after they experimented on and failed to turn him into a Super Soldier? Offscreen Moment of Awesome?
- Wham Line:Scully: You are as false as your face. I bet you wish night and day that that bullet that was meant to kill you had succeeded.
- Wham Shot: 'Daniel Miller' looking at his ruined reflection in the interrogation room glass, followed by a Match Cut to Jeffrey Spender moments before CSM shot him in the head.
- Wounded Gazelle Gambit: Although Jeffrey's burns and wounds are very real, he played up his condition and situation for all it was worth to garner sympathy from the X-Files team and gain access to William.