S8E2 · Without

FBI special agent Fox Mulder (David Duchovny) is currently missing, having been abducted by aliens in the seventh season finale, " Requiem." His partner Dana Scully (Gillian Anderson) has been working with Agent John Doggett (Robert Patrick) in order to locate him. After consulting with The Lone Gunmen, a trio of conspiracy theorists made up of John Byers (Bruce Harwood), Melvin Frohike (Tom Braidwood) and Richard Langly (Dean Haglund), Scully finds evidence that Mulder may be in Arizona. Doggett receives news that Gibson Praise (Jeff Gulka), a boy with potentially extraterrestrial DNA, may be in hiding in Arizona as well. The two, along with Walter Skinner (Mitch Pileggi) and a task force of FBI agents arrive and, after searching, find Mulder and Praise on the corner of a mountain.

Doggett pursues Mulder and Praise and corners them at the edge of a cliff. Doggett convinces Mulder to release Praise who runs off alone, but Mulder intentionally steps off the precipice and apparently falls to his death. When agents go to retrieve the body, they only find footprints. Scully realizes "Mulder" was an Alien Bounty Hunter sent to retrieve Praise.

While the Alien Bounty Hunter returns to the school to continue his search for Praise, Scully follows Praise's schoolmate, a deaf girl named Thea (Christine Firkins), through the desert to a hidden underground room. Praise has broken his leg reaching the hiding place. Scully applies first aid, but is unable to move him without a car.

After Doggett explains the events on the cliff to Alvin Kersh, Skinner tells him that Kersh is setting him up to fail. Shortly afterwards, the Alien Bounty Hunter (now disguised as Scully) attacks Agent Landau. Skinner and the real Scully eventually manage to drive the alien away. Later, Skinner gets Praise to a hospital, but leaves Scully behind in the desert.

Searching for Mulder in the desert, Scully sees a bright light in the sky which is revealed to be a helicopter with Doggett inside. Doggett insists Scully travel with him to the hospital; she reluctantly accepts. There, two other FBI agents assure them that nothing has happened to Praise; however, they soon discover that he has vanished. Scully leaves to search for Praise while Doggett stays in an attempt to catch the intruder. He checks the ceiling space, where he finds Skinner badly injured. Scully finds Praise with "Skinner" who claims to be protecting the boy. The Alien Bounty Hunter attempts to kill her, but Scully shoots and kills him first.

After reporting to Kersh, Doggett is assigned to the X-Files with Scully. Meanwhile, Mulder continues to be held in captivity, experimented on and tortured as six Bounty Hunters look on.