A police car races down the highway in Bellefleur, Oregon. In the driver's seat is Detective Miles (last seen in the "Pilot" episode), who radios to his deputy, Ray Hoese, that he is approaching with backup on a downed aircraft in the woods. Suddenly, the digital clock scrolls backwards. The car loses power as it careens into another sheriff's cruiser, parked on the side of the road. A dazed and injured Detective Miles gets out of his car. A big fire burns in the distance through the trees. He notices the hands on his wristwatch are spinning backwards, as he approaches the other vehicle. An unconscious Ray Hoese slumps over the wheel. The deputy's eyes are swollen shut, the lids and membranes blistered and burned. Detective Miles looks down to see he has stepped in a bubbling, green substance. When he turns around, another Deputy Hoese stands before him. The man's eyes are unscathed. This Hoese has three bullet holes in his chest with the same green substance oozing out of him. Miles recoils in horror.

In Washington, Mulder sits before a large pile of receipts. Agent Chesty Short, the deputy chief auditor of the FBI, admonishes both Mulder and Scully for the extravagant expenses racked up by the X-files. He questions what they are investigating, now that the Samantha case has been resolved. Back in their office, the agents receive a call from Billy Miles (from the "Pilot"), who reports that the abduction experiences are occurring again. This time, however, they are not happening to him.

Two teenagers scour the Oregon forest in an excited search for a UFO. One of the boys steps into an invisible force field and gets shaken at warp speed. Spooked by this sudden disappearance, the boy's friend Richie drops his flashlight, which has suddenly become red hot, and runs out of the woods.

Marita Covarrubias releases Krycek from a Tunisian prison on orders from the Cigarette-Smoking Man. The pair find the CSM near death, in a wheelchair, and attended by a nurse. Krycek is furious with the old man for sentencing him to a foreign jail. The CSM is eager to report that an alien ship collided with a military aircraft in Oregon. He needs them to recover it. "Our chance to rebuild the project," he whispers with a faint voice squeezed through a neck shunt.

Determined to rebuke Agent Short and spend more of the FBI's money, Mulder and Scully set off to Oregon to meet with Billy Miles, who is now a sheriff's deputy. The unidentified craft has yet to be found, and Deputy Hoese is still missing. Billy's father, Detective Miles, claims that there was never another craft. The agents follow the Miles officers to the scene. At the spot where Detective Miles' car went dead, Mulder sees an "X" spray painted on the pavement. It is the same mark he made on the road seven years prior to designate an anomalous electrical disturbance. Scully locates shells on the ground from Hoese's gun, but there is no indication of what he might have been shooting at. The agents drive off, and Detective Miles puts the evidence bag in his trunk -- next to the body of Ray Hoese. Mulder and Scully visit Hoese's wife, Teresa, and are surprised to find she is an abduction victim who approached them for help seven years ago. She says that her husband is also an abductee who had been taken and tested many times. As Scully holds Teresa's baby, Mulder watches his partner. The sight of Scully with a child seemingly has an effect on him.

Scully comes to Mulder's motel room later that evening, pale and perspiring, suffering from chills. He covers her up in his bed and lies with his arms around her for warmth. "It's not worth it, Scully," he says. He's been thinking that her personal costs are too high when motherhood and her health have been taken away from her. He demands that there has to be an end. Outside the motel, Krycek sits behind the wheel of a parked car. He is on the phone to the CSM, telling him that no one can find the spaceship, even as Mulder and Scully search for the deputy. The CSM assures him that the ship is really there. Finding the deputy will uncover the ship. The CSM hangs up with Krycek, and Marita asks why he has him on a goose chase. "The ship is rebuilding itself," the CSM says. Ever faithful that his minion will be successful, the CSM is only wary of Krycek's true intentions once he finds the ship. Across town, Teresa Hoese is awakened by the return of her missing husband. When Ray doesn't speak to her, she realizes that he is only an imposter. She gashes him with a pair of scissors, but the stabs don't faze him. Green ooze bubbles from the holes in his chest, causing Teresa's eyes to burn and blister. She stumbles and is grabbed by the imposter.

The next morning, Billy reports to Mulder and Scully that Teresa is missing. They immediately recognize the green acid burn on the floor, and as Scully touches it, she experiences another wave of vertigo. Outside the Hoese home, Mulder and Billy spot Richie eyeing the crime scene. Richie admits that "they" took his friend, and that Detective Miles does know what's going on because he was there. Richie leads the agents to the area in the forest where his friend vanished. Scully is quickly jerked into a force field and shook at a high frequency. Noticing Scully is missing, Mulder calls out for her. She lies on the ground semi-conscious, as if from another bout of vertigo. As Mulder cradles his partner's head, Scully questions why this is happening to her. Mulder determines that these aren't merely random abductions, but a case of abductees not coming back.

A suspicious Billy returns home and draws his gun on the man that appears to be his father. "I don't know who you are, but you're not going to take me," he proclaims. Detective Miles calms his son before morphing into the Alien Bounty Hunter. At the same time, Mulder and Scully enter the house to warn Billy. Both men have instantly vanished.

Mulder sits in his FBI office two days later, when Skinner enters with Krycek and Marita. There is a moment of complete surprise, but Mulder's quickly out of his chair to attack his nemesis. They explain that the CSM is dying, but his final wish is to revive the conspiracy. While the Bounty Hunter eliminates proof of testing on abductees, the spaceship, cloaked in an energy field, rebuilds itself. That evening, the Lone Gunmen are brought in to Skinner's office to consult. They determine the ship's location even though the military has not picked it up on satellites. Mulder listens suspiciously to Krycek and Marita in silence. Scully abruptly leaves the room and Mulder follows her into the hallway. Since they are reclaiming abductees, he refuses to allow her go back to Oregon. "I won't risk losing you, Scully," he says. She hugs him, vowing that she won't let him make the journey alone.

Scully remains in Washington with the Lone Gunmen, scrutinizing the abductee reports. Each one has reported experiencing the same irregular brain activity that struck Mulder earlier in the year. She concludes that Mulder is really the one in danger of being taken. Without warning, Scully collapses, and the Gunmen jump to save her. Meanwhile, Mulder and Skinner enter the Oregon forest. They lay out a series of laser pointers to detect any abnormal movements. As Mulder follows the red beams, something catches his eye. The red lines deflect in space and define the rough shape of a dome, but it seems as if they are colliding with an energy field. Mulder reaches out to touch the field and his hand vibrates at a high speed. Looking up from laying down the last laser pointer, Skinner notices that Mulder is gone. Inside the field, a bright cone of light reflects on Mulder. His expression is full of awe. The other abductees are there to greet him with gentle smiles. A spaceship hovers overhead, and the Bounty Hunter enters the circle of abductees. The light grows in intensity and Mulder's look of awe turns to fear. Outside the force field, Skinner is unaware of this activity and calls out for Mulder. All of a sudden, a spaceship appears from out of nowhere and Skinner watches it rise into the night sky. He is left alone in the darkness.

Krycek reports back to the CSM that he failed his mission, but the CSM suggests that perhaps Krycek never meant to succeed. As Marita watches, Krycek shoves the CSM's wheelchair down a flight of stairs. The Cigarette-Smoking Man's body lies on the ground, motionless and apparently dead.

The next morning, Skinner is awkward when he visits Scully in her hospital room. She is better, but waiting on more tests. Skinner tries to hold back his emotion in telling her that he lost Mulder. She takes his hand and says she already heard the news. "What I saw I can't deny. I won't," he promises. They both begin to cry, and Scully assures him that she must find her partner. "There is something else," she says to Skinner. Although she can't explain it or believe it herself, she is pregnant.

TO BE CONTINUED...