The beginning is a strange way to put it. But it’s true. We start with a strange occurrence involving a Bounty Hunter who, in true ‘alien’ style, happens to have a creature burst out of his body, killing a scientist from ‘Roush’ and disappearing to the local Power station. Meanwhile, Mulder is attempting to pick up where he left of by recovering whatever remains of his office still exist. He attempts to explain to the FBI why he wants to continue his work on the X-Files, however after reading his report relating to the events he saw during the X-Files movie, they don’t really believe his work to be creditable, and doesn’t manage to convince them that he should continue working.
His last ace – the evidence Scully uncovers regarding the virus she was infected with being extra-terrestrial, doesn’t work. Scully cannot identify the virus, but she does know that the DNA is very much of planet Earth, and couldn’t possibly create an alien being. The Smoking man is back with the security council, and they have wind of the Bounty Hunter’s virus infection. Skinner informs Mulder that that his request to continue working on the X-Files has been denied. But we know Skinner is on his side when he points Mulder to a folder on his desk which leads him to the alien in the Power plant. On visiting his old office, Mulder finds Agent Spender down there, who informs Mulder he is no longer the owner of that office, and that the person who will be working with Spender is… Diana!
Back on her feet and stabbing Mulder in the back. Agent Mulder and Scully make it to the power plant, they state to Spender who stops them that Skinner has told them about a man who’s died. Diana doesn’t let them in either, stating they are there because of a connection to other deaths.. from a case file stolen from their office….! Diana then goes to see Mulder, stating she took the job because she wanted to make sure someone kept working on the X-Files properly, and that since she started the X-Files with Mulder, she took it to keep him in the loop, and offers to take him to the power plant to find the creature. Mulder believes her and they both head over to find it.
Meanwhile, Scully takes Gibson… who’s returned mysteriously in their car, to hospital. While at the hospital, Scully finds results of Gibson’s blood test.. he’s infected with the same virus Scully was infected with. Gibson then gets taken from the hospital and to the power plant, because he can communicate with the creature… Mulder and Diana watch as the creature attacks the man escorting Gibson, while Gibson runs for cover, Diana draws her weapon on Mulder, and a whole host of people converge on the power plant. To end the story, Mulder’s back at a hearing, Skinner isn’t there, for reasons we’ll see later.
They are told that both Agent Mulder and Scully are to desist any association with the X-Files, and they are now to report to a new Assistant Direct…. Assistant Direct Kersh. We finally see Smoking man congratulating Spender on the way he handled Mulder, and the alien mutates into a fully fledged grey alien.