THREE WORDS

Under the cover of darkness, an unidentified man jumps over the fence to the White House and is intercepted by Secret Service personnel. As he struggles with them, he pulls a gun and accidentally shoots himself. Bleeding on the ground, the man hands over a computer disk, begging them to give it to the President. Three words are written on the disk: "FIGHT THE FUTURE".

Fox Mulder (David Duchovny) is in his office, recalling how he was tortured on the alien ship. Dana Scully (Gillian Anderson) enters with Dr. Lim and they give him surprisingly good news: The neurological condition that was killing him, before his disappearance, is gone and 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. Meanwhile, in prison, an inmate librarian gives former UFO cult leader Absalom a book about the apocalypse. Hidden inside is a newspaper article about the man who jumped the fence. Absalom later escapes during a work detail by attacking a guard with a board with a nail in it.

At FBI Headquarters, Deputy Director Alvin Kersh informs John Doggett (Robert Patrick) and Walter Skinner (Mitch Pileggi) that Mulder has applied for reinstatement to the X-Files. He intends to deny the request, claiming a higher percentage of success with Doggett. Kersh ignores Doggett and Skinner's defenses of Mulder, perceiving him to be a crusader unfit for proper Bureau work. Doggett later finds Absalom waiting for him at home with a gun, demanding that Doggett show the back of his neck to confirm his identity. He tells Doggett that the man killed at the White House, Howard Salt, died for what he knew about an alien invasion.

Absalom duct tapes his gun to Doggett's back in a plan to get Salt's information, with Doggett used as a hostage. The two attempt to sneak into the census bureau's database, which Absalom claims contains data showing the aliens are already here. Unfortunately, the plan fails when an X-ray scanner detects the gun. Absalom is shot and killed by security. Mulder later accuses Doggett of deliberately attempting to cover up the truth by setting up Absalom to be killed, to which Doggett takes great offense. Doggett later meets with his liaison, Knowle Rohrer, who reveals the password to the census bureau is "Fight the Future."

Scully, on Doggett's request, tells Mulder that the disk was labeled “Fight the Future.” Mulder realizes that this is the password and breaks into the census bureau with the help of The Lone Gunmen, searching computer data. Doggett soon arrives, realizing that the password leak was a trap. After a bitter argument (and upon both Scully and the Gunmen revealing to Mulder the arrival of black ops mercenaries on the scene), they are forced to leave. Doggett confronts Rohrer about the false tip, but Rohrer claims he was just trying to help Doggett learn the truth. As Doggett and Skinner leave, strange protrusions are seen at the back of Rohrer's neck

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