In 1973, the Syndicate presents a folded American flag to alien representatives as a symbol of collaboration. Back in the present, a decontamination team from the CDC that includes Fowley bursts in and sends the agents and Cassandra to a quarantine facility, saying they've been exposed to a contagion of unknown origin. Scully, pointing out that Cassandra's been in a hospital for a long time, is suspicious of Fowley and thinks it's an attempt to isolate Cassandra.
Cancer Man says the Syndicate needs to turn over Cassandra to the aliens to save themselves and get the loved ones they sacrificed to the extraterrestrials returned. Mulder finds Marita at the facility looking pretty sickly, and she says the hybrid program was never intended to succeed, but only to buy time to make a vaccine. She also says colonization will begin if the aliens learn Cassandra is a successful hybrid.
Mulder sneaks into Fowley's apartment and finds Cancer Man, who tells him that Spender has decided to throw in his lot with Mulder. Cancer Man says the Syndicate has saved billions of lives by forestalling alien invasion, and denies Mulder's accusation that they're just trying to save their own asses. He says they needed to give up family members (Samantha taken belatedly) in order to get the alien fetus to make a vaccine from. He says the colonization will begin after a state of emergency is declared following an outbreak of the alien virus via bees and handing over Cassandra is the only way people will survive.
Spender finds the Syndicate's headquarters in New York City abandoned, and Krycek tells him they've moved to West Virginia to prepare for colonization and taken Cassandra with them. Cassandra begs Cancer Man to kill her, again in vain. Fowler returns to her apartment to find Mulder still there, rattled at what Cancer Man has told him. Cancer Man has also given him a piece of paper with "El Rico Air Force Base" written on it, and says they need to be there if they want to survive.
An alien rebel kills a doctor working with the alien fetus. Mulder wants Scully to come to the base with them, but Scully says she's going to the train yard to try to stop Cassandra's transportation (information she got by Spender, who got it from Marita). Mulder tells Fowley to go ahead, and he and Scully try unsuccessfully to stop the train, which includes a rebel in disguise.
Krycek finds that the rebels have stolen the fetus and refuses to help Spender try to rescue Marita, saying everything's going to hell and the rebels are going to win. At El Rico, the Syndicate and their families have gathered, along with Cassandra and Fowley. The base doors open, and realizing that something's wrong, Fowley and Cancer Man book it. Alien rebels storm the place and kill everyone left in the hangar. Kersh is horrified by the deaths, and Spender urges him to put Mulder and Scully back on the X-Files. Spender finds Cancer Man in his office, reminiscing about how Mulder's father was a friend who betrayed him. Cancer Man then shoots Spender.
Episode Body Count
Doctor: killed by an alien rebel disguised as a nurse.
Cassandra Spender and at least 25 Syndicate members and relatives: it's tough to count due to the low light in the hangar, but it's a relatively low Syndicate count and a fair amount of family members.
Jeffrey Spender: shot and killed by Cancer Man.
Cumulative Body Count (129/202 episodes, 1/2 movies)
Humans: 1,514Creatures: 100
Grand Total: 1,676