Federal census worker Howard Salt hops over the fence at the White House, and a squadron of Secret Service agents ambushes him. "The aliens are taking over the United States!" he exclaims. Suddenly a gunshot goes off, and the agents realize Salt has accidentally shot himself. Before succumbing to death, he hands one agent a CD-ROM with the words "Fight the Future" written on it.

In his hospital room, Mulder puts his hand on his face and chest scars, seeing flashbacks of the alien torture he endured. Scully interrupts these visions when she tells him that he is completely healthy and miraculously healed of whatever brain disorder he may have suffered. She takes him back to his apartment, which is still intact. "I don't know if you'll ever understand what it was like," a visibly moved Scully acknowledges. Mulder, however, is still unsettled, not knowing how he fits in his newly restored life.

Skinner and Doggett are summoned to Kersh's office to be briefed about Mulder's reinstatement to the X-files. Because of Doggett's success rate of arrests, Kersh is prepared to deny Mulder's application. He orders the two to tell Mulder that he is off the X-files. Doggett resists and Kersh threatens to shut down the X-files altogether. Skinner and Scully come to Mulder's apartment to bring him the bad news. Mulder first learns of Agent Doggett's assignment to the X-files and realizes that they have all become pawns in some larger conspiracy. He gets up to get dressed, telling Scully and Skinner, "For the first time, I feel like getting back to work."

At a Federal Correction Facility in West Virginia, a trusty brings Absalom a book entitled "The Coming Apocalypse." Inside is a newspaper clipping about Howard Salt being killed when he jumped the White House gate. Later, as the prisoners work on a roadside gang, Absalom breaks away and escapes into the woods. That night, Doggett returns home to find Absalom waiting for him. Absalom checks the back of the agent's neck for traces of reptilian-looking alien vertebrae. "You're going to spread the word," he tells Doggett before kidnapping him. From the FBI, Scully tries unsuccessfully to reach Doggett while Skinner briefs his task force on the hunt for Absalom. Skinner tells the agents that the man's claims of alien invasion are to be taken seriously. He shows them a photo of the words "Fight the Future" scrawled on Absalom's cell wall. Scully and Skinner find Mulder in the X-files office. He has picked out Howard Salt's face in an Absalom cult photo and informs them that Salt was a multiple abductee. Mulder is convinced that the man was killed for what he knew. Mulder and Scully sneak into the FBI Evidence Room to discover Howard Salt's laptop computer has its entire memory filled with an encrypted program. Mulder removes the hard drive.

With a gun taped to the small of his back, Doggett enters the Federal Statistics Center. Absalom's hand is on the trigger. When passing the security guard, Doggett notices the x-ray scanner and warns Absalom that they will be stopped. Absalom pushes Doggett on, saying that he is looking for proof that aliens are "already here, among us." Security guards quickly surround them, and Doggett is shocked when they shoot Absalom, nearly missing Doggett's head. Later, when Doggett briefs Skinner on the previous events, Mulder bursts into the office. Doggett is about to introduce himself when Mulder attacks him. He blames Doggett for getting Absalom killed, suspecting that he is part of the conspiracy to hide the truth.

At Scully's apartment, the Lone Gunmen tap into Salt's hard drive and unearth file directories from the Statistics Center. Fifteen minutes after Salt's death, computer firewalls had gone up around the facility. Mulder is convinced that he is onto something in those files. However, even if they were to uncover a password, the firewalls would block them from opening the files. The pass code can only be used in the secured facility itself. Much to the consternation of Mulder, the Gunmen agree with Scully that they have hit a dead end. Meanwhile, Doggett secretly meets with his informant Knowle Rohrer (last seen in 8X08) to ask why Absalom was shot in cold blood. Doggett suspects that he was merely used to get the man killed. Rohrer tells him that there are three words he should know. Doggett meets Scully outside Mulder's apartment, asking her to give Mulder information he has recently learned. Salt was carrying a diskette that he wanted to give to the President. The password on it contains three words: Fight the Future. Scully goes back into Mulder's apartment but is hesitant to tell him what Doggett told her. She fears that he will get in over his head. Skinner rushes to Doggett's house that night with urgent news about Mulder having some kind of password to access names tracked by the government. When Doggett admits to giving Scully the password, Skinner begins to question whose side Doggett is on. He is even more concerned because he can't contact either Scully or Mulder. "You're gonna have to trust me on this," Doggett tells the Assistant Director and sets out after them alone.

Doggett finds Scully outside the Statistics Center and orders her to leave. "I may have set you up," he pleads. He runs inside to get Mulder out. The Gunmen, meanwhile, have bypassed the security system to allow Mulder access to the building undetected. They lead him into the databank and Mulder types the words "Fight the Future" in the computer. Doggett bangs on the glass door, but Mulder ignores him. "Your life's in danger!" Doggett yells and blows out the window with his gun. Doubting Doggett's intentions, Mulder says that he believes the government is using the census to protect aliens in hiding. Armed military troops storm the building, and Mulder accuses Doggett of setting him up. Doggett tries to convince him that really they have both been set up and are in danger. The Gunmen direct Mulder and Doggett toward an air duct in the ceiling, and they escape.

Doggett again covertly meets with Rohrer and accuses the informant of manipulating him. "You need me worse than you know," Rohrer says emphatically. He tells Doggett that the truth lies in the X-files. An angry Doggett walks away. When Rohrer leans over to the water fountain, enlarged alien vertebrae pop up under the skin on his neck.