Aware his presence only puts Scully and William in jeopardy Mulder once again disappears ? but at least this time it is his own choice. A frustrated Agent Doggett tries to find Mulder so he can proceed with his investigation against Deputy Director Kersh, but Scully and Skinner finally convince him to drop his case.
Mulder is missing and assumed dead
although Scully experiences a vision in which he is still alive.
After Mulder's disappearance, Scully returns to FBI headquarters to find Special Agent John Doggett heading up a FBI manhunt for her partner.
As Mulder lies in a neurological unit, his brain under attack by a deadly onslaught of electrical impulses, Scully struggles to decipher strange symbols covering a spacecraft found submerged off West Africa's Ivory Coast. But the connection between these two phenomena is just the first of many challenges the agents are destined to confront.
Two agents from vastly different backgrounds join forces to solve cases the FBI has labeled X-Files.
After Scully helps him fake his own death, Mulder breaks into The Pentagon and obtains a metal vial containing a chip that will ultimately prove to be a cure for Scully's cancer. Scully forms a bond with Cassandra Spender, a woman who claims to have been abducted by aliens multiple times.
The X-Files has been shut down and Mulder and Scully are separated. Scully finds herself teaching classes at the FBI Academy in Quantico, Virginia, while Mulder is assigned to surveillance duty.
After Mulder's informant X is shot and killed by the Syndicate, he finds a valuable new ally. Mulder and Krycek travel to Tunguska, where Mulder is captured and imprisoned. Russian researchers infect Mulder with the black oil -- only to miraculously cure him. When Scully is diagnosed with inoperable brain cancer, Mulder becomes convinced that the disease is linked to her alien abduction.
When a terrorist bomb destroys a building in Dallas, Texas FBI agents Fox Mulder and Dana Scully are drawn into a dangerous conspiracy surpassing anything they've ever encountered.