Howard Salt, a US Census worker, breaks in to the White House grounds to warn that aliens are taking over America. As he is shot by a guard, Salt hands him a CD labelled 'Fight the Future'.

Scully has requested that Mulder be re-assigned to the X Files, as he is now free of viruses. Kersh meets with Skinner and Doggett, saying he wanted to speak to them before denying the request - angering Doggett, who must tell Mulder. Skinner later tells Mulder that Kersh wants to punish him, and will keep the X Files open with Doggett at the helm.

Absalom, now in gaol, makes an escape bid whilst part of a chain gang. A passing train allows him to outrun his guards. Armed, he surprises Doggett in his apartment.

Skinner, Scully and Mulder investigate Absalom's escape. Looking at a photograph of Absalom, Mulder notices Howard Salt in the background. Skinner realises he's right, and Mulder doubts that Doggett would have spotted the connection. Later, in an evidence room, Mulder seizes the hard-drive from Howard Salt's laptop - it is full of encrypted files.

Absalom tapes a gun to Doggett's back, the barrel pointing at his head. He takes Doggett to an information processing complex, where he wants to view US Census data for proof of alien infiltration. The pair are attacked by a SWAT team, and Absalom is killed.

Arriving at the complex, Mulder accuses Doggett of covering up the truth and helping to kill Absalom. Doggett is dumbstruck - the bullet that killed Mulder nearly hit him.

The lone Gunmen decrypt Howard Salt's data - it's from a government data bank. However, after the White House break-in, new firewalls have been installed - to access more data, pass codes will be needed. Doggett meets Knowle Rohrer, who gives him the pass code - Fight the Future. Doggett passes the phrase on to Scully.

Later, Skinner tells Doggett that the passcode let Mulder break in to a database of people whose genetic profile makes them abduction targets. Making his way to the complex, Doggett tells Scully that he may have inadvertently set up Mulder.

Mulder has infiltrated the complex with help from the Lone gunmen. As he accesses a computer, Doggett arrives, and shoots his way into the locked room. Mulder handcuffs himself to the desk as Doggett confronts him, but Scully sends word that a SWAT team are on their way. Doggett tells Mulder that they've been set up, and will be killed by the SWAT team. Langly confirms this - and tells them that the data that Mulder had emailed out has been caught in a data trap and will never reach the press. They escape through a ventilation shaft as the SWAT team break in.

Later, Doggett meets Knowle Rohrer again, and threatens to expose him unless he tells him everything he knows. Rohrer says that his is a minor player, and Doggett leaves. Rohrer stoops to take a drink, and shows a strange, reptilian vertebra beneath his skin...

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