Mulder is about to pull the trigger and end Cassandra Spender's life, when the door to his apartment is forced open and CDC agents storm in, taking Mulder, Scully and Cassandra into custody.

In a quarantined area at Ft. Marlene military base, Mulder and Scully are addressed by Diana Fowley. She explains that Cassandra Spender had contracted a highly contagious virus and needed to be put in isolation pending full medical evaluation. Scully scoffs at this notion, calling it unjustified and highly suspicious. Scully believes that Cassandra was taken so that the tests could continue. Mulder tells Scully that the tests won't continue because they have been completed; Cassandra is, in fact, the first successful human/alien hybrid. Cassandra knew this and was begging Mulder to end her life so that the aliens would not start colonization.

In a hallway at Ft. Marlene, Mulder finds Marita Covarrubias. She appears haggard and quite ill. She tells Mulder that they have been performing tests on her to find a vaccine against the Black Oil. She explains to Mulder that the hybrid program was in cooperation with the aliens, but the conspirators never intended to succeed. They were only buying time until a vaccine was created to fight the Black Oil. But now that Cassandra Spender is a successful human/alien hybrid, colonization will begin.

Scully calls Mulder to the Lone Gunmen's lair where she tells him of her suspicions about Diana Fowley. Scully feels that Diana is somehow working with the Syndicate, but Mulder refuses to believe her. Scully storms out and Mulder pays a visit to Diana's apartment. He begins searching her room for any incriminating evidence when the CSM enters the apartment. Mulder holds him at gunpoint as CSM substantiates the entire Syndicate operation. He even explains that Mulder's father gave over Mulder's sister Samantha to the aliens as a guarantee of their honor. In return, the aliens gave the Syndicate the alien fetus that would allow the human/alien hybrid work to begin. CSM truly believes that what he did saved millions of lives and ultimately would bring Samantha and other family members back home. It was Mulder's father who thought of the idea to use the alien fetus DNA to make a secret vaccine against the Black Oil.

Jeffrey Spender pays a visit to his father in the Syndicate offices, only to find Krycek in the now abandoned space. Krycek tells Spender that everyone has left for El Rico Air Force Base to receive the hybrid genes and that Spender's father, CSM, has gone to get Cassandra to turn her over to the aliens. Spender informs Scully. Meanwhile, Mulder and Diana, who has returned to her apartment, leave for the base. Mulder calls Scully to have her meet them there. Scully tells Mulder about Cassandra and the two rush to intercept the train. The train plows through their car as they escape the impact.

Diana joins the Syndicate in the hangar at the base, and Cassandra is brought in. The doors open and the rebel aliens enter, incinerating the Syndicate and their families. Diana and the CSM manage to slip out. Later, Spender takes responsibility for the deaths and recommends to A.D. Kersh that Mulder and Scully be reinstated on the X-files. The CSM enters Spender's office to confront his son. Spender expresses his hatred for the CSM. The CSM draws his gun and points it at Spender. After firing a single shot, the CSM exits.