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In a dream-like sequence, Dana Scully walks through a desert and picks up a gold cross necklace on the ground. Continuing from the previous episode, agent Fox Mulder arrives at the hospital in San Diego where Scully introduces him to Emily. Mulder tells Scully that he had Melvin Frohike look into Emily's case: her surrogate mother is a woman named Anna Fugazzi (slang for fake), and there are no true records of how Emily came into the world. Mulder, along with Scully's family, attend a meeting regarding Emily's adoption at the San Diego Hall of Justice. Mulder tells the Judge that Emily was conceived from Scully's ova, which was taken from her during her abduction, which the Judge does not believe. Later, Scully receives a call from the County Children's Center that cuts off abruptly. She and Mulder head there, where they find Emily safe, but coming down with a fever. They find a greenish cyst on the back of Emily's neck. Later, when a nurse pierces the cyst with a needle, green liquid comes out, causing her to become gravely ill, yet Emily appears unaffected. Mulder believes that Emily has the same body chemistry that they have seen before with alien-human hybrids.
Dr. Calderon, Emily's doctor who works for a company called Prangen, refuses to transfer Emily's medical records to the County Children's Center, prompting Mulder to rough him up, but has to leave when security arrives. Later, Mulder follows Calderon after he leaves his office. Scully has imaging tests conducted on Emily. Calderon goes to see the Dark Suited Men, one of whom kills him by stabbing him in the neck with an alien stiletto; both men then morph into Calderon. Mulder follows as one of them leaves. The results of Emily's tests show her to be suffering from a tumorous infection. The other Calderon arrives at the hospital and injects Emily with an unknown green substance; he escapes by morphing into someone else. Scully believes that he is continuing the treatments, and the Sims were murdered because they were trying to stop him. Mulder follows the first Calderon clone into a building, where he meets Anna Fugazzi, an elderly woman in a nursing home.
The doctor tells Scully that Emily is getting worse. A woman from the adoption agency arrives and 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, and deceives Mulder and escapes. Mulder returns to the hospital, where Emily has gone into a coma. Days later Emily has died. 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.
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