S5E7 · Emily

In a dream-like sequence, Dana Scully (Gillian Anderson) walks through a desert and picks up a gold cross necklace on the ground.

Continuing from the previous episode, agent Fox Mulder (David Duchovny) arrives at San Diego County Children's Center, where Scully introduces him to Emily. Mulder tells Scully that Emily's surrogate mother is named Anna Fugazzi, but that fugazzi is slang for fake, and there are no true records of how Emily came into the world.

Mulder is interviewed by a judge, regarding Scully adopting Emily. Mulder explains that Emily was conceived from Scully's ova, which were taken from her during her abduction; the judge is skeptical. Later, Scully and Mulder find that Emily has a fever, and they discover a green cyst on the back of her neck. In a hospital, a nurse pierces the cyst with a needle, and green liquid oozes from the wound. The nurse collapses from exposure to the liquid, but Emily appears unaffected. Mulder believes that Emily has the same body chemistry that they have seen before with alien-human hybrids.

At Prangen Pharmaceuticals, Mulder tries to get Dr. Calderon, Emily's doctor, to grant access to Emily's medical records; Calderon refuses. Mulder beats him up and threatens him with a gun. Calderon hurriedly leaves the building; Mulder follows, surreptitiously. Scully has imaging tests conducted on Emily.

Calderon goes to a large house to see the two Dark Suited Men, one of whom kills him by stabbing him in the back of the neck with an alien stiletto. Calderon's wound bleeds the same green liquid. Both men then morph into Calderon look-alikes. Mulder follows one of the look-alikes as he leaves the house. The results of Emily's tests show her to be suffering from a rapidly-growing neoplastic mass in her central nervous system. The second Calderon look-alike injects Emily with an unknown dark green substance, then escapes by changing his appearance again. Scully believes that Calderon is continuing the treatments, and that the Sims were murdered because they were trying to stop him. Mulder returns to the large house, which turns out to be a nursing home. There, he stumbles upon the real Anna Fugazzi, an innocent elderly lady.

The hospital doctor tells Scully that Emily is getting worse. A woman from the adoption agency wants to stop Scully from making decisions for Emily. Mulder connects the names of the women in the nursing home to recent births and finds that Dr. Calderon was treating them. Emily reacts badly to being placed in a hyperbaric oxygen chamber. Mulder finds medical records with Scully's name on them at the nursing home, along with a live fetus in a refrigerated chamber. Mulder finds Calderon entering soon after, and Detective Kresge arrives as well. Mulder and Kresge confront Calderon, who attacks Kresge. Despite Mulder's warning, Kresge shoots Calderon, whose wounds cause him to spew green blood which incapacitates Kresge. Mulder quickly leaves the building to avoid being affected by the blood. Calderon morphs into Kresge, deceives Mulder, and escapes.

Mulder returns to the hospital, where Emily has gone into a coma. Days later Emily dies. Mulder visits Scully at the funeral chapel, telling her that Kresge is recovering and all evidence at the nursing home and Prangen is gone. The only evidence left is Emily's body, but the agents instead find sand bags in her coffin along with Scully's cross necklace, which she had previously given to Emily.