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Scully mysteriously reappears in a Washington hospital, alive but in a coma. Knowing that she had signed a last will and testament wishing to end her life if she was in such a state, Mulder works against the clock and looks for evidence on who did this to his partner and how he bring her out of the coma.
Mr. X: I didn't expect you here till after visiting hours.
Mulder: There was a man. He took Scully's blood.
Mr. X: Forget him.
Mulder: Get that gun out of my face.
Mr. X: This high capacity compact Sig Sauer 40 caliber weapon is pointed at your head to stress my insistence that your search for who put your partner on that respirator desist immediately.
Mulder: You ignore my call for help and then you expect me to do what you say. You can go to hell.
Mr. X: You got him killed. You got her killed. That's not going to happen to me. You're my tool, you understand? I come to you when I need you.
Mulder's apartment number is 42, but in a scene, it appears as 4.
Although, Skinner has a no smoking sign in his office, there seems to be ashtrays all around his office.
Freeze-Frame time: Mulder's signature on the hospital paperwork is different than the handwriting on his photo ID as shown in the opening credits.
Why didn't the doctors notice the large hole in Scully's abdomen? Or the branched DNA?
"Hewlett Packard" has been taped over on Mulder's laser printer, leaving only "LaserJet 4" to be seen.