Written by Chris Carter
Summary by Keleka and Shoshana
Internal dataing: None, there's virtually no way to pinpoint an exact time of year for this episode.
A man writhes painfully, surrounded by murky golden liquid. He struggles to breathe, succeeding only after expelling an umbilical-like tube from his mouth. His features are now visible--it's Fox Mulder. Scully wakes from her nightmare vision, disoriented for brief seconds before realizing it was only a dream. Her hand moves protectively to her abdomen, instinctively protecting her unborn child.
Scully dresses in front of her mirror the next morning, unsure the reflection she sees is truly the woman she was just the day before. She strides down a hallway in the Hoover building, acutely conscious she is alone; that the office she has shared with Fox Mulder for the last seven years will be a cold. empty place today. But when she arrives, she doesn't find the solitude she expected. Instead, she finds anonymous men rummaging through the contents of the X-Files filing cabinets. They won't find clues to Mulder's disappearance by searching his office, she tells them.
She finds Skinner in his office, hanging up the phone in anger after learning of the search after-the-face. He promises Scully he will find Mulder and doesn't want her to do anything to put her pregnancy at risk. They are summoned to see their new boss, the recently appointed new Deputy Director, Alvin Kersh, their former nemesis from the sixth season. Kersh demands their full cooperation in the search for Mulder by a task force headed by Special Agent John Doggett. In a parting shot, he threatens their jobs if one word of aliens or alien abductions leaves the building.
Skinner wants to tell the truth--he knows what he saw and does not want to sell Mulder out--but Scully cautions him to obfuscate. She reminds him that he won't be much help to her or Mulder if his career is ruined. Scully waits uneasily while Skinner gives his statement to an agent. A man two seats down from her engages her in conversation. He claims to have known Mulder and questions Scully's true knowledge of her partner's affairs, including his relationships with women at the Bureau. The man dismisses the rumors about her ambition, and lack of trust between them. Scully smells a rat, flipping John Doggett's badge over and confronting him. Disgusted with his trickery, she throws a glass of water in his face and leaves the room.
At home, Scully researches Doggett's background, discovering he is a former Marine and New York City policeman. Scully becomes nauseated while reading the information, then rushes to the bathroom to vomit, presumably from morning sickness. She calls her mother later, leaving a poignant message which conveys her loneliness. She hears a clicking sound on the line and suspects a wiretap.
She spies a man across the street from her apartment, watching her through the window. She calls Doggett's number, demanding that he stay out of her life, but Doggett doesn't seem to comprehend. Shadowy footsteps outside her apartment door bring her senses to full alert. She unholsters her gun and gives chase, following the figure to the end of a hallway. A man is on a scaffolding beside the window, but it's her landlord, not an intruder. He claims to have seen Mulder in the building minutes before.
Scully races back to her apartment, calling out Mulder's name with hopeful anxiety. But no one is there and her laptop has been stolen. She leaves for Mulder's apartment and when she arrives, she enters hesitantly, as one might when entering the domain of a newly deceased loved one. Mulder's computer is also missing. She enters his bedroom, her expression revealing. Perhaps she is thinking of time she's spent in this room, in this bed, in recent months. She picks up a wrinkled dress shirt from the bed, clutching it to her chest, a weary, empty look in her eyes as she lies on Mulder's bed. She closes her eyes and dreams of Mulder, bound to a chair, his face pulled taut by wire hooks. A mechanical device enters his mouth, drilling into his upper palate. He screams in pain, unable to escape his bonds.
Meanwhile, Skinner meets with the Lone Gunmen near some satellite dishes which they have hacked their way into. They are intercepting data about UFO activity across the Pacific Northwest since Mulder's disappearance. Despite their efforts, there is no way to pinpoint the spacecraft's next destination. Back at the Hoover Building, Doggett confronts Kersh, curious whether someone else is assigned to his case. Kersh denies anyone else is involved, but the look on his face after Doggett exits suggests he has not been completely truthful to his task force leader.
The next morning, in Mulder's apartment, Scully awakes to find Doggett standing in the bedroom doorway, watching her. She thinks he has tailed her there, and confronts him about tapping her phone and demanding he treat her with respect. He lets her know she won't get his respect until he gets hers, and he denies tapping her phone. They circle each other warily, dancing around the question of whether Scully believes Mulder was abducted by aliens. She comes as close as she ever has to admitting she does.
Doggett has come to Mulder's apartment to search for clues about his disappearance. He shows her car rental receipts for trips to Raleigh, North Carolina. He wants to know why Mulder travelled there for four successive weekends in May. Scully doesn't offer any information on the matter, claiming ignorance of the trips. Their conversation is interrupted by a call to Doggett from FBI headquarters. Someone has used Mulder's passcard to steal files from the building. They leave immediately for the Hoover Building.
Skinner is interrogated by task force members about the possibility he is aiding Mulder by using his card. Skinner denies this indignantly. Doggett tells Scully he believes Skinner's story, but doesn't know what to make of charges on Mulder's credit card made two days ago. She tells him Tena Mulder is buried in Raleigh, a possible explanation for the charges.
Doggett has a crate rolled in, then opens it to reveal a Mulder family monument. It is engraved with birth and death dates of all family members, including Mulder's--1961-2000. Scully eyes the engraving woefully, not knowing what to make of its significance. Doggett shows Scully medical records detailing Mulder's slow decline in health since his brain surgery in fall of 1999. He was being treated by doctors for side effects of the anomalous brain activity he'd experienced after contact with the artifact. Scully seems to believe the documents are the real thing, as shocking as that may be to her.
Doggett wants to know how far Mulder would go to validate his work--would he take one last chance to prove his work was legitimate by faking his own death? Could he have stolen the computers and files to cover up his disappearance and raise doubt about his whereabouts? Skinner protests, saying he knows what he saw near Bellefleur, Oregon, and that he watched Mulder be abducted by an alien vessel. Scully--her expression one of anxiety and fear for Skinner--asks Doggett not to report Skinner's remarks to anyone. Doggett seems to agree, saying it doesn't help him find Mulder anyway.
The Lone Gunmen meet Scully and Skinner in his office, showing them evidence the space ship may be in the Arizona desert, north of Phoenix. Langly posits the aliens are looking for another abductee. Scully has a Mulder-like leap of intuition and realizes it must be Gibson Praise, the young boy who disappeared from a nuclear reactor several years ago. Gibson's DNA proves aliens exists; if they are covering up evidence, he would be a logical target.
While the agents consult with the Gunmen, Doggett notices a file slipped underneath his office door. It is information on Gibson, stolen from the FBI the previous evening. Doggett addresses his task force members, advising them of Gibson's importance to Mulder. The agents laugh when he tells them Gibson is thought to read minds, but he tells them they must head out to Arizona to find Mulder.
In the next scene we once again see Mulder, bound to an examination table. A medical saw descends to his chest as he cries out in terror. Scully is jolted awake by the image and we discover she was napping while Skinner drives through the Arizona desert. They have satellite data which shows UFO activity one hundred miles north of Phoenix. They are oblivious to helicopters flying above them, one of which is transporting Doggett to the area. He is notified by one of his agents that Gibson Praise is at the Flemingtown School for the Deaf. He directs the chopper to head over there.
Scully sees ripples in the atmosphere above the desert. She doesn't know whether she's hallucinating from the intense heat or actually witnessing a disturbance in the air from a force field. It is the alien ship, but she discounts the experience, not trusting her own eyes. She agrees with Skinner they should visit a school for the deaf he has just found on the map.
Gibson is pulled out of class by a school official after exchanging a meaningful look with a female classmate. Doggett arrives at the school, but Gibson has slipped away from the office he was occupying. Scully and Skinner arrive moments later, astonished to see Doggett is already there. Scully asks Doggett what he is doing there and he replies, as he runs out the door, that he is trying to find Mulder.
Gibson is shown sneaking out the back, then bumping into an unidentified man outside the school. As the task force agents spread out around the building, Doggett discovers two sets of footprints, headed for the mountains near the school. Doggett gives chase, thens yells at a man restraining Gibson. The man has his back to Doggett, and when he turns around, it is clearly Mulder.