Doggett catches someone in the X-files office trying to steal documents pertaining to Mulder's sister. The intruder is a severely scarred man who blames his disfigurement on Government conspirators. He claims the source of that information - and, in fact, the one who helped him gain entry - is Mulder. Although he refuses to divulge the missing agent's whereabouts, the mystery man has enough knowledge of the X-files and its history to lead Doggett to suspect that he just might be Mulder himself. Scully's fears for the safety of her son are elevated when he is injected with an unknown substance. With the mystery surrounding William becoming even darker, Scully must allow herself to send him away for his own safety.
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.