The X-Files, season 2

Separated and reassigned, both of them keep working the same problem from opposite ends — Mulder on surveillance detail he ignores, Scully teaching at Quantico. A new source appears and proves less reliable than the last. The office they were thrown out of turns out to be easier to close than the thing it was investigating.

The season turns on a man named Duane Barry, who says he was taken repeatedly and is desperate not to be taken again. What he does about it puts Scully in a car she does not get out of. She is gone for weeks. When she is found, it is in a hospital bed with no explanation of how she got there, and what was done to her in the interval is not something anyone will say. She recovers. She is not the same, and neither is her body.

From there the work stops being about proving that something is happening and starts being about who is running it. There are people being grown, or copied — Mulder meets a man with his own face on someone else's body, and then meets several more. A bounty hunter moves through the story killing them methodically, and the government's interest in stopping him is conspicuously absent.

By the end Mulder has his father's involvement in front of him and a tape full of documents he cannot read. His father does not survive the conversation they were about to have. The season closes in the desert with Mulder inside a buried railway car full of bodies and someone above ground deciding what to do about him.