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Three months after Mulder's death, the body of Billy Miles, a man abducted at the same time as Mulder, is found in the ocean. Just as he's about to be autopsied, he seemingly comes back from the dead - turns out, he was never really dead, his vitals were just slowed to virtually undetectable levels. This leads Skinner to believe Mulder may also still be alive.
- Affectionate Gesture to the Head: Scully puts her hand through Mulder's hair.
- Artistic License Medicine: Mulder was apparently in a sort of coma for three months while buried, his life signs barely detectable, but without water or nutrients to sustain him. Only alien science can explain it away.
- Bait-and-Switch: When Mulder finally wakes up, he asks Scully who she is. This leads us into thinking that his abduction gave him severe amnesia, but when he smiles at her response, we can all breathe a sigh of relief.
- Body Horror: Billy's skin peeling away in the shower is one of the more disturbing images on the show.
- Cry into Chest: Scully to Mulder as he lies in the hospital.
- Death Glare: Doggett gives Krycek an epic one when Krycek mockingly drops the vaccine to cure Mulder.
- Faking Amnesia: Jokingly, Mulder pretends to not know who Scully is for a brief moment when he wakes up in the hospital.
- Held Gaze: Mulder and Scully when he wakes up in the hospital.
- Holding Hands: Scully holds Mulder's hand while he's unconscious, and he twitches to show he's awake.
- Pet the Dog: Despite how much of a jerkass Kersh was in the past and going forward, he attends Mulder's funeral and is genuinely solemn. A possible hint of his eventual HeelFace Turn.
- Reports of My Death Were Greatly Exaggerated: Everyone has believed Mulder to be dead for the last three months. Not too far off from the truth, but in reality he's just been in a sort of coma, with vital signs so weak they were undetectable.
- Sadistic Choice: Krycek offers Skinner the vaccine that will save Mulder's life, but to get it Skinner must kill Scully's unborn baby.
- Shout-Out: Robert Patrick pursuing a fleeing car on foot while attacking them in a parking garage. Sound familiar?
- Time Skip: The beginning of the episode shows Mulder's funeral, then skips to three months later.
- Unrequited Love: Heavily implied from Doggett to Scully over the course of their time working together, and that she knows. For his part, Doggett never acknowledges it to her verbally, sharing a look at the end of the episode with her that sums it up, realistically understanding the futility of it, that her heart already belongs to Mulder.
- Unbroken Vigil: Scully finds out Mulder is alive and at the hospital, and verbally chews out anyone who says she shouldn't be there or she should leave.