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.