In a railroad yard in Arlington, Virginia, doctors in biocontainment suits make an incision in a patient's stomach. Green acid boils out and the cut heals itself. Another doctor arrives and is told that after 25 years the work is complete, but a faceless man arrives and sets fire to the medical team. We see that the patient is Cassandra Spender, who has been missing for a year.

The Cigarette Smoking Man discusses the conspiracy for his unseen guest. It is hard to believe that the end is here. It was a perfect conspiracy, preparing the way for the invasion of an alien race and creating a slave race of human-alien hybrids. They kept it secret for 50 years but a rebel alien race came to upset their plans.

Skinner tells agent Spender that his mother is in the hospital, having survived the attack in the rail car. At the hospital, she does not explain what happened but asks to talk to agent Mulder. Not happy about it, Spender eventually asks Mulder for help, but Mulder believes that it is a set-up, designed to entrap Mulder and get him out of the FBI completely. Meanwhile, the Smoking Man visits the one doctor who survived the rail car attack. He is in a hyperbaric chamber because of his burns. The doctor says the rebels came to take Cassandra so they can expose the conspiracy. The doctor points out that he must not be questioned, and with regrets, the Smoking Man turns off his oxygen supply. In Silver Spring, Maryland, one of the elders (played by actor George Murdock) is informed by the Smoking Man that an emergency meeting of the Consortium has been called, but a faceless man arrives and burns the elder.

Mulder and Scully realize that they have seen these burned bodies before and that Scully has been kidnapped and subjected to tests in a rail car in the past. They meet with Cassandra in secret at the hospital. Long confined to a wheelchair, she can now work fine and feels wonderful. She says the woman Mulder saw last year was not his sister. Samantha is with the aliens. The doctors were also working with the aliens who are here to wipe the human race off the planet. They are taking over the universe, infecting all other life forms with a black substance called "purity," which is their life force. Agent Spender is also in danger, because he is allied with the men who are working with the aliens, Cassandra says.

The Smoking Man tells his unseen guest that he killed to keep his collegues from finding Cassandra because he couldn't bring himself to allow the death of his ex-wife, and that his collegues did not realize that their group had been infiltrated. In the meeting of the consortium, we see the burned elder alive and well. He suggests that the consortium should ally with the rebels but Krycek refutes the suggestion, saying that helping the invaders has provided time to develop a way to fight them. At the FBI, Mulder and Scully use Spender's computer to research Cassandra and agent Spender. They locate a photograph of Cassandra's ex-husband, C.G.B. Spender, and it is the Smoking Man. Skinner warns them to leave the X-Files office, but Spender arrives with other men and Mulder and Scully are put on administrative leave for unauthorized access to the X-Files office.

Spender reports to his father that Mulder has been suspended. They argue and Spender is told "you pale to Fox Mulder." But later, because he has been exposed, the Smoking Man goes back to Spender and assigns him to kill the rebel masquerading as an elder, using an "ice pick" weapon. Krycek drives Spender to the Elder's mansion but Spender bungles the attack and Krycek barges in and kills the alien. Spender is shocked at proof of his mother's claims. Krycek admits that Cassandra has been the subject of experiments for 25 years and that agent Spender has, in effect, been protecting the project that has harmed his mother. Meanwhile, Scully has researched C.G.B. Spender. The name is certainly an alias, but Scully has a box full of information, including a 1973 photograph of C.G.B. and Bill Mulder. They worked together for 25 years on a classified project and it is clear that the project is still going on. We finally learn that the Cigarette Smoking Man has been talking to Diana Fowley. He says she has never failed him and she answers that it's not too late, she will help.

Cassandra is not in her hospital room and her guard is gone. She shows up at Mulder's apartment, scared because "they" are right behind her. As someone else knocks on Mulder's door, Cassandra says she is "the one," and tells Mulder she must kill her. As the pounding on Mulder's door continues, and as Scully says "no, we have to protect her," Mulder draws his gun and aims at Cassandra. To be continued, next week.