Although Mulder is denied reassignment to the X-files, he nevertheless investigates a man who was shot before he could inform the President that an alien invasion has begun.
A man puts on black gloves and climbs the White House fence. While reporters photograph him bemusedly, he runs at the White House and is intercepted by the Secret Service ERT. As he struggles with them, he pulls out a gun and accidentally shoots himself. Bleeding on the ground, he begs the agents to get something to the President and hands them a computer disk with three words on it: Fight the Future.
Mulder remembers his experiences on the alien ship as he touches the scars on his face and chest. Scully enters with Dr. Lim and they give him surprisingly good news, especially given he was in a coffin until recently: The neurological condition that was killing him, before his disappearance, is gone, the virus he contracted recently is gone, and his scars are healing fast. He is in perfect health.
Mulder returns to his apartment with Scully and he congratulates her on the pregnancy she had sought for a long time. He is a bit distant; a lot has happened and he hasn’t processed it all yet.
In prison, the inmate librarian gives Absalom a book about the apocalypse with a newspaper article hidden within about the man who jumped the fence.
Deputy Director Alvin Kersh calls Agent John Doggett and Assistant Director Skinner into his office. He informs them that he has received an application for reinstatement to the X-Files from Fox Mulder and that he intends to deny the request, claiming a higher percentage of success with Doggett. Though Skinner and Doggett defend Mulder, Kersh clearly is uninterested in restoring Mulder because he perceives him as a crusader.
While Mulder talks about getting back to work, Absalom escapes from his prison work detail by attacking a guard with a board with a nail in it.
Agent Doggett returns home after work and finds Absalom waiting for him with a gun. Absalom demands Doggett show the back of his neck to confirm that Doggett is still himself. He tells Doggett that the man killed at the White House, Howard Salt, died for what he knew about an alien invasion.
Meanwhile, Skinner directs the manhunt of Absalom before he and Agent Scully are called down to the X-Files offices by Mulder. Mulder shows them that Howard Salt was one of the abductees that Absalom knew and that the census worker must have known something important that got him killed.
Absalom duct tapes his gun to Doggett’s back in a plan to get Salt’s information with Doggett used as a hostage. Mulder removes the hard drive of Salt’s laptop from the FBI evidence room. Absalom’s attempt to get into the server room with Doggett fails because of an X-Ray scanner detecting the gun. He claims that the census bureau had data which showed the aliens were already here. Security shoots Absalom through the head despite his use of Doggett as a body shield.
Doggett and Skinner discuss the death of Absalom when Mulder comes in and shoves Doggett, accusing him of setting Absalom up to die. Mulder goes to see the Lone Gunmen at Scully’s house. They decrypt the hard drive of Howard Salt and find out it had data downloaded from the Federal Statistic Center. Now high level firewalls protect the center and one would need to access the data on site. They recommend Mulder give up this time. He refuses.
Agent John Doggett meets with his informant, Knowle Rohrer, to ask if he was indeed used to get that man killed. Rohrer cryptically says that what Doggett is dealing with is far above anything he’s dealt with before and that he can only tell him three words: Fight the Future.
Doggett goes to see Mulder but knows he won’t listen so he has Scully tell him about the disk labeled “Fight the Future” that the census worker had and how those three words are a pass code for the databank. After she gives the tip to Mulder, she realizes she shouldn’t have told him because he will use the code but she goes on the fool’s errand nonetheless.
Skinner wakes up Doggett because he can’t reach Mulder or Scully. Skinner tells Doggett that it is about information on the census tracking people with specific genetic backgrounds.
Doggett shows up at the Federal Statistics Center and tries to convince Scully to leave, claiming he set them up to be killed unintentionally due to the information he passed on.
Mulder slips into the Center with the help of Langly, Byers, and Frohike hacking the security systems. He begins searching the data on the computers, as Doggett arrives to warn him, shooting his way into the server room. Mulder claims certain people have been targeted for abduction and replacement by facsimiles based on their genetics.
As they are talking, the troops begin to arrive to murder them both in cold blood. Mulder doesn’t believe Doggett is trying to save him but Scully calls the three Lone Gunmen and they explain that there are troops approaching as seen on the security cameras. Langly tells Mulder the data is trapped and they aren’t managing to get anything uploaded. Byers explains to Mulder and Doggett how to get out of the server room through the ventilation system.
John Doggett confronts Knowle Rohrer about the tip he gave but Rohrer claims he was just trying to help Doggett learn the truth. As Doggett and Skinner leave, it can be seen that Rohrer has strange protrusions at the back of his neck.
- The title of this episode refers to the three words, "Fight the Future". Here, the words are a password that allows access to a highly sought-after computer disc but they were previously used as a common tagline of The X-Files Movie.
- While trying to enter the databank as Absalom holds him hostage, Doggett shows the guard his badge upside down.
- David Duchovny as Special Agent Fox Mulder
- Gillian Anderson as Special Agent Dana Scully
- Robert Patrick as Special Agent John Doggett
- James Pickens, Jr. as Deputy Director Alvin Kersh
- Tom Braidwood as Melvin Frohike
- Dean Haglund as Richard Langly
- Bruce Harwood as John Fitzgerald Byers
- Judson Scott as Absalom
- Adam Baldwin as Knowle Rohrer
- Nelson Mashita as Dr. Lim
- Gary Bristow as Howard Salt
- Joe Basile as Lead Guard
- Ric Sarabia as Marion
- Dwight Hicks as Armed Prison Guard
- J.C. Murad as Intercom Guard