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 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. It ends with Mulder pushing him over a ledge and down a few flights onto electrical wires, supposedly killing him. Some guards take Mulder to a jail. Skinner tells Scully that Mulder is back and they 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. Later, 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 but in a military court of law. Scully and Skinner go to see Mulder, with no guard this time, and 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. Then, 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. Later, scully visits Mulder alone in his cell. She says she needs him to tell her the truth of they'll lose. Mulder says he's been hiding in New Mexico, looking for the truh. He says he found something in the facility earlier but he won't tell her what. The next day, the trial begins. Skinner is upset because it's a military court of law and because he can't find Marita Covarrubias, his first witness, so he calls Scully to the stand. She talks about how she came to the X-Files, how she believes in aliens, and how there are government conspiracies. Next, Skinner calls Jeffrey Spender. Spender talks about the Cigarette Smoking Man, Mulder's sister, and abductions. Later, in his cell, Scully begs him to make them a deal or something but he refuses. When she leaves, X appears. He gives him information on how to find Marita Covarrubias. Skinner calls her next. She talked about alien viruses & vaccinations, Krycek, and the Syndicate. Skinner then calls Gibson Praise. Gibson says he hid Mulder in the desert for the last year. Gibson then reveals that one of the judges is a super-soldier. 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 talked about Scully's baby. 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. 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 get to Scully and Gibson. Kersh tells Mulder and Scully to go to Canada and be off the continent in 24 hours. The next morning, Doggett and Reyes find that their office and the X-Files have been packed up. 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 something in the rocks out there. The agents barely make it out alive before black helicopters blow up the puelos 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 crawled into bed together and held each other.

they all died. Heroicly. But still.

did they kill them? Why why why? what gets me even more is that they killed them off without mulder anywhere in sight to bid them a fawn fairwell

Kill the lone gunmen off in a season or episode where Mulder isn't even around makes me feel sad. Such great friends and he couldn't have been there to morn or anything. this is why that season doesn't exist to me anymore.

Did they really die tho? I always had the impression that TLG were actually alive. That the toxin was a sham and that their funerals were fake and they are now stuck working for the government or some special thing or whatever.