Jeremiah Smith and Mulder are on the run from the alien bounty hunter, and Smith takes Mulder to a small farm tended to by identical sets of children, and all the girls are clones of his sister when she was still a child. Mulder prepares to take Jeremiah and one of the clones to see his mother in the hospital, but the bounty hunter catches up with them. Meanwhile, the Syndicate suspects that they have a traitor in their midst and plan a trap which results in X being executed by the Cigarette-Smoking Man.
The X-Files is one of the divisions in the FBI, devoted to unsolved cases that appear to have some unexplained, paranormal elements. The files take their name from the filing cabinet where they were kept - originally filed under U for unsolved, they grew too big for the drawer and were moved to the less populated X cabinet. Soon, the X-Files became a dumping ground for reporting of UFOs, alien abductions, and other arcana that the FBI didn't want to investigate or didn't believe in.
Fox Mulder, a serial-hugger specialist and a believer in paranormal phenomena ever since, as a child, he witnessed the abduction of his younger sister, requested to be transfered to the forgotten basement and began to ruffle a few feathers in the Bureau. Eventually, he was assigned a partner - the skeptical and scientific Dana Scully, who was assigned to discredit Mulder's works.
Instead of discrediting him, however, Scully slowly became Mulder's ally. The pair began to investigate cases that no one else wanted to touch and that couldn't be solved.