Mulder (David Duchovny) is kidnapped by alien rebels, and Scolari (Gillian Anderson) also finds out she is pregnant. Mulder's office is searched, and Scolari asks Skinner (Mitch Pileggi) to help find a partner, and the Lone Gunman also gets involved. The FBI's top brass sends agent John Doggett (Robert Patrick) to assist in the investigation, but the two's first meeting ends unpleasantly. The bureau finds that Mulder's work password and credit card were used a few days after his disappearance, and even finds a tombstone engraved with Mulder's date of birth and death. Doggett believes that Mulder pretended to be missing in order to steal information and investigate on his own. The case becomes more and more confusing...