THE TRUTH

At the Mount Weather military base, Fox Mulder (David Duchovny) appears with several government officials. He gains access to highly classified documents on a secure computer system, and is shocked and dismayed to read the documents, which provide details of the final colonization of the planet by alien forces. Before he can continue reading, Mulder hears another person approaching. He hides quickly and observes Knowle Rohrer (Adam Baldwin), a former friend of John Doggett (Robert Patrick) but who has been irreversibly transformed into an enemy "Super Soldier", approach the computer system. Rohrer immediately realizes the system has been accessed. Mulder attempts to attack Rohrer, but Rohrer overpowers him. Mulder frantically flees, but Rohrer outflanks him. In a violent altercation, Mulder flips Rohrer off a catwalk onto high-voltage wiring, and Rohrer apparently dies by electrocution. Mulder attempts to escape, but is quickly arrested by several soldiers.

News of Mulder's arrest spreads to the FBI. Upon hearing that he has resurfaced, and in such a dire manner, Dana Scully (Gillian Anderson) and Walter Skinner (Mitch Pileggi) visit him in military custody. During his time in captivity, Mulder receives mysterious visits from two phantoms of his past: Alex Krycek (Nicholas Lea) and X (Steven Williams). Meanwhile, Scully and Skinner go to great lengths to get him released, but are unsuccessful. Mulder's fate is ultimately made the subject of a military tribunal with Deputy Director Alvin Kersh (James Pickens, Jr.) in charge. At the outset, it appears Mulder will become the hopeless victim of a show trial stacked against him.

Skinner takes Mulder's defense, while Scully, Doggett, Monica Reyes (Annabeth Gish), Marita Covarrubias (Laurie Holden), Gibson Praise (Jeff Gulka) and Jeffrey Spender (Chris Owens) testify on Mulder's behalf. The prosecution presents Rohrer's body as evidence against Mulder. Aware that Rohrer is a seemingly-invincible "Super Soldier", Scully performs a medical examination and proves that the body is not that of Rohrer. Despite this, the evidence is rejected, given that the autopsy was not authorized, and the defense is overruled. Mulder is sentenced to death for the murder of a military officer. Later, Doggett, Skinner, Reyes, and Scully help Mulder escape, with the unexpected help of Kersh who decided he should have let Mulder go in the first place. Despite being advised to immediately leave the continent via Canada, Mulder instead takes Scully to New Mexico. On their way, Mulder receives a visit by three additional ghosts: The Lone Gunmen, who advise him to flee for his life rather than continue his pursuit of the truth. Mulder politely declines. Meanwhile, Doggett and Reyes find their office emptied, suggesting that the X-Files have been closed down for the third time.

Mulder and Scully arrive at Anasazi ruins to find a "wise man" who they believe can make sense of the classified documents Mulder has read. They discover the so-called "wise man" is none other than The Smoking Man (William B. Davis), who, still alive after all, is hiding out to survive the colonization—an event that will happen on December 22, 2012, the predicted end of the world. Outside, Reyes and Doggett arrive and prepare to fight Rohrer, who has been sent to kill Mulder and The Smoking Man. Rohrer is killed when the magnetite in the ruins affects his superhuman body. Switching cars with Mulder and Scully, Doggett and Reyes drive off. Black helicopters destroy the cliff dwellings—and The Smoking Man within—thinking that Mulder is still inside before flying away. Doggett and Reyes are last seen speeding away.

In a motel room in Roswell, New Mexico, Mulder and Scully prepare for bed and talk. Mulder explains his belief "that the dead are not lost to us. That they speak to us as part of something greater than us—greater than any alien force. And if you and I are powerless now, I want to believe that if we listen to what's speaking, it can give us the power to save ourselves." Despite their slim chance for success, Mulder declares, "Maybe there's hope", as they lay back, content in each other's arms, in a loving embrace.

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