Summary:
Mulder breaks into a secret government facility. He is discovered and when the chase is on, he kills one of the guards who is attacking him (up on a catwalk, the guard was choking him and Mulder did a clever foot move and the guard went flying over the railing onto electric powerlines).
Mulder is given a military trial for murder. The judge gets approached by a senior ranking military officer who tells him no matter what to convict Mulder. Skully and Skinner are called in, Skinner to represent Mulder. Skinner tries to show that Mulder has been the brunt of a top secret conspiracy and that his attempt to uncover the truth was what resulted in the guard's death. Mulder knows something that he keeps from disclosing to Scully and Skinner, "for their own good". Several witnesses come forth but they are discredited. One of them was the little kid who could read minds. He said one of the judges was an alien. Another witness told of the Syndicate, a top secret conspiracy where those in power were calling the shots and trying to make an alien/human hybrid. All of these people present their side but are discredited for one reason or another.
Mulder is convicted and sentenced to death by lethal injection.
Skinner, Scully and the judge help Mulder break out of prison before his punishment can be exacted. Skinner tells him to run to Canada, but Mulder and Scully head off to some Indian ruins to seek the real truth. When they get there to the deserted Indian ruins, they find Mr. X who is sitting in a secret cave looking like one of the grateful dead. He explains what Mulder already knew but didn't want to tell Scully. That an alien invasion was going to take place in the year 2012 and that it had happened before. He said that the U.S. was trying to invent some super soldiers who were hybrids. He then said that there was a secret facility where all the world's leaders were going to go when the invasion took place and that they would be safe from the invasion, but the rest of the world would not.
Scully and Mulder leave about the time Doggett and partner arrive to tell them the military is coming after them. They leave in a hurry about the time a bunch of gunships blow up the Indian ruins and Mr. X.
The scene ends with Scully and Mulder sitting in a motel room talking about the search for truth and how the past few years were worth it because they had found each other. I gather that they were assumed dead and will try and go into hiding, but that their x-file work is done.