Scully has been abducted so Mulder must race to find Duane Barry before he finds what appear to be the aliens that are in his head.

Mulder, tired, enters his apartment and plays back his answering machine. Scully speaks about the alien implant she is in possession when suddenly she screams for Mulder's help. Mulder rushes over to Scully's appartment where he finds the police searching her place for evidence. He also finds Scully's mother, Margaret distraught that her daughter has been taken away.

Meanwhile, Duane Barry drives along the highway with Scully trapped in the trunk of the car. A patrolman pulls him over because he was driving too fast. When the patrolman catches a glimpse of Barry's fingers which are covered in blood, he pulls out his gun and asks him to exit the vehicle. When he is distracted by Scully's screaming, Barry shoots him and drives off.

Luckily the incident was caught on tape so Mulder analyses the footage and finds that Scully is still alive. This strengthens his search for Scully so listening back to what Duane said while Mulder was interviewing him, he realizes that "Ascending to the stars" is in fact the description of Skyland Mountain and so goes there with Krycek just after his sneaky new partner had informed the Cancer Man of where they were going.

At the mountain, Mulder convinces the aerial tram operator to let Mulder go up on the tram despite the fact that he could be killed. Just before Mulder reaches the top, Krycek kills the operator and stops the tram stranding Mulder out there. As he climbs onto the top of the tram, Krycek starts it up again hoping to kill him but Mulder survives and rushes to where Duane is. Mulder arrests Duane who is ecstatic that the "aliens" have taken someone else, Scully. Mulder later talks to Duane who says that "they took her. Suddenly, Mulder spots a piece of ginger hair with blood on on Duane's wrist so Mulder pounces on him nearly choking him.

Krycek enters the room after Mulder's exit and after he leaves and Skinner appears, Duane goes into cardiac arrest and dies. Later, Krycek meets with the Cancer Man again and Krycek asks him "Why they don't just eliminate Mulder?". The Cancer Man cooly replies "That will risk turning one man's religion into a crusade".

At the meeting of the incident with Duane, Mulder thinks that Duane was poisoned by Krycek while he was in the room and that the results of his autopsy are being covered up because of this. Mulder tries to contact Senator Matheson for help taking Krycek's car, but Mr. X intervenes and says that the senator can't help him without "committing political suicide". When Mulder returns to Krycek's car he notices a certain number of Morley cigarettes in his ashtray.

Back at the FBI headquarters, he accuses to Skinner that Krycek is responsible of poisoning Duane and killing the tram operator. Skinner tries to contact him but finds that he has mysteriously vanished. This prompts him to do what "they fear the most", re-open the X-Files.

Later, Mulder meets with Scully's mother and offers the cross he found which belonged to Dana. She replies "You give it to her when you find her". If he finds her.....