Investigating evidence of an alien autopsy, Mulder infiltrates a secretive government train carriage carrying an alien-human hybrid. Mulder is almost killed by a Syndicate operative guarding the hybrid, but is saved by his informant X. X had been tipped off about Mulder's activities by the agent's partner Dana Scully. Scully, meanwhile, meets a group of women with abduction experiences similar to her own, and meets another member of the Syndicate known as the First Elder, who claims during her abduction she was placed on a similar train car and experimented upon by the Japanese scientists. The crew of a French salvage ship trying to raise a World War II-era submarine from the sea floor are stricken with massive radiation burns—except for one, who has been infected with a parasitic black oil discovered on the submarine. The oil is controlling the crewman's body, and after passing through several hosts, has overtaken Alex Krycek, who Mulder has been pursuing. Scully finds that the submarine had been involved in discovering the oil on the sea floor during World War II, under the guise of finding a sunken fighter plane. The infected Krycek makes his way to a missile silo used to hide a UFO, and the oil escapes his body to board the craft. Meanwhile, Scully has tracked down Luis Cardinal, the man responsible for killing her sister.
