Mulder arrives in a helicopter along with other people at the Mount Weather Complex, a government building, in Bluemont, VA. The people are guided along inside but Mulder escapes. He sees he's in some sort of facility so he looks around. He enters a secured area and looks on a computer and sees something startling but before he could do anything, Knowle Rohrer finds him. They fight but Mulder escapes and then Knowle starts chasing after Mulder. Then, Krycek appears and helps Mulder out. Knowle Rohrer catches up with Mulder and they fight some more and Mulder pushing him over a ledge and down a few flights onto electrical wires, supposedly killing him. Some guards catch up and take Mulder to a holding cell. In his cell, Mulder is continuously questioned and tortured by the guards until he confesses that he broke into the facility. Skinner and Scully come to visit him in jail. In their meeting, Mulder seems passive and non-expressive and appears to be brainwashed. He tells them he's a guilty man and should be punished. After Scully and Skinner leave the room, Krycek appears and starts talking with Mulder. Scully and Skinner inform Doggett and Reyes of the situation. Scully and Skinner go back to see Mulder, with no guard this time, and he says that he had to put on an act last time and isn't really brainwashed. Mulder and Scully share a long kiss. Skinner tells Mulder that he's on trial for his life. Mulder says they're rigging the case and asks Skinner to represent him. Skinner accepts. Doggett and Reyes come in with news that the military claims to have the body of Knowle Rohrer, which the agents know is impossible since super-soldiers can't die. Kersh goes to the USMC Base Brig in Quantico and asks for the military to go easy on Mulder. Kersh is told that Mulder will get a trial in a military court of law but it will be preformed by the F.B.I. Later, Scully visits Mulder alone in his cell. She says she needs him to tell her the truth or they'll lose. Mulder says he's been hiding in New Mexico, looking for the truth. He says he found something in the facility earlier but he won't tell her what. The next day, the trial begins and Skinner meets the prosecutor Agent Kalembrenner. Skinner is asks for a dismissal because it's a military court of law which violates Mulder's right to a fair trail but is denied. He then asks for a continuance because he can't locate his first witness Marita Covarrubias but is once again denied, so he calls Scully to the stand. She talks about how she came to the X-Files to debunk Mulder's theories but she now believes in aliens, and how there are government conspiracies to cover up their existence. Next, Skinner calls Jeffrey Spender. Spender talks about his father, the Cigarette Smoking Man, and the abduction and eventual death of Mulder's sister at the hands of CSM. Later, in his cell, Scully begs Mulder to make a deal or something but he refuses. When she leaves, X appears and gives him information on how to find Marita Covarrubias. Skinner calls her next and she talks about the alien viruses & vaccinations, Krycek, and the Syndicate. Skinner asks if she knows who the men are that are involved in the current conspiracy but Krycek appear and tells Mulder to stop her or they will kill her. Skinner is reluctant but agrees and dismisses her. Skinner calls Gibson Praise to the stand. Gibson says he has hidden Mulder in the desert for the last year. Skinner explains to the court that Gibson has the power to read minds because his DNA is part alien. Kalembrenner asks if he can read the minds of the judges and Gibson then reveals that one of the judges is a super-soldier. Mulder demands an examination of the man but is escorted out of the room. In his cell, Mulder talks to Skinner, Doggett, and Reyes. Skinner asks Mulder to testify but he refuses but Doggett and Reyes volunteer. Skinner calls Doggett to the stand. Doggett says Mulder couldn't have killed Knowle Rohrer because he couldn't be killed. Skinner calls Reyes next. She talks about the birth of Scully's baby and the importance of the baby to the super-soldiers. That night, Scully and Reyes go to see the supposed body of Knowle Rohrer. Scully finds hard evidence that the body is not Knowle Rohrer and takes it to court since it could get Mulder out but then Kersh throws out the evidence and adjourns the trail. The next day, the panel finds Mulder guilty. Scully later gets a call that night that Mulder's sentence is death by lethal injection. That night, Doggett and Skinner come to break Mulder out of jail. When they get near the exit, Kersh finds them but helps them escape. They meet up with Scully and Gibson. Kersh tells Mulder and Scully to go to Canada and be off the continent in 24 hours. Mulder proceeds south and tells Scully he has to see a man about the truth. The next morning, Doggett and Reyes find that their office and the X-Files have been packed up. They go to get an explanation from Kersh and the super-soldier judge opens the door. Gibson reads his mind and discovers that he knows where Mulder and Scully are really going and they plan to kill them. On the drive to New Mexico, Mulder pulls over to go the bathroom when the Lone Gunmen appear. They tell Mulder to turn around and leave but he doesn't want to. Later, Mulder and Scully get to some pueblos. They go inside and find the Cigarette Smoking Man, alive. He tells Scully what Mulder found on that computer in the government base, that on December 22, 2012, the aliens will invade and take over the world. Meanwhile, Doggett and Reyes get to the pueblos but Knowle Rohrer finds them and tries to kill them but is destroyed himself because of the Magnetite in the rocks. The agents barely make it out alive before black helicopters blow up the pueblos with the Cigarette Smoking Man inside. Mulder and Scully go to a hotel in Roswell and talk. Mulder says he's failed in every aspect but Scully disagrees. She says he'll never give up. And she said she'd do the last 9 years all over again. Then, they crawl into bed together and hold each other.