Scully comes to terms with the shocking revelation that a mysterious little girl is her daughter, although the details surrounding her creation are horrifically sinister and unforgiving.
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 Sim. Mulder tells Scully that Melvin Frohike has found that Emily's surrogate mother is a woman named Anna Fugazzi and that 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 ovum, which was taken from her during her abduction, which he has a hard time believing. Later, Scully receives an abandoned call from the County Children's Center, and 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. Emily appears unaffected. Mulder believes that Emily has the same body chemistry that they have seen before with alien-human hybrids.
Dr. Ernest Calderon refuses to transfer Emily's medical records to the County Children's Center, causing Mulder to visit him and rough him up when he refuses to do anything. 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 a stiletto. Both men 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 something. He escapes by morphing into someone else. Scully believes that he is trying to continue the treatments and that the Sims were murdered because they were trying to stop him. Mulder heads to a building he saw Calderon going to, 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 suffers from a terrible reaction after being placed in a hyperbaric oxygen chamber. Mulder finds medical records with Scully's name on them at the nursing home. He also finds a fetus in a refrigerated chamber. Mulder finds Calderon entering soon after, and Detective John Kresge arrives as well. Mulder warns Kresge not to shoot him, but he does so anyway after Calderon attacks him and green blood comes out of him. Calderon morphs into Kresge and is able to trick Mulder into letting him leave. Mulder returns to the hospital, where Emily has gone into a coma. Days later Emily has passed away. Mulder visits Scully at the funeral chapel, telling her that Kresge has recovered and all evidence at the nursing home and Transgen is gone. The only evidence left is Emily's body, but the agents find sand bags and the cross Scully gave her earlier in her coffin, which she picks up.
- The animated program seen on the hospital television is "Life With Louie," a Fox animated series hosted by comedian Louie Anderson. This was the one of several instances in season 5 that other Fox shows were featured in the background of episodes.
- One of the mothers Frohike names had a child born on September 25th, 1994, the same day that Gillian Anderson gave birth to her daughter, Piper Maru.
- In a heartbreaking off-screen dilemma for the crew, Emily was originally played by a bright, energetic 4-year-old girl. Her scenes in the first part didn't require much dialogue and the child did fine. Unfortunately, when the time came to film the scenes in the hospital with Emily being given a CAT Scan, the little girl was so frightened by her surroundings she couldn't be comforted or calmed enough to be able to film the shot. In what he ponders to be the worst thing he has ever done in the business, Executive Producer Robert Goodwin was forced to recast the part and luckily they were able to find slightly older Lauren Diewold in time to finish filming.
- The second set of MRIs on Emily show a date of 10/31/97 when it should be sometime between Christmas and New Year.
- Mulder says that Scully was abducted and missing for four weeks. In 'Duane Barry' the date stamp is given as August, In the episode "Emily." We know that Scully was gone in October by the date stamp in Charmaine Villard's paperwork. It clearly says Scully, DK 13.10.94. In '3' when Mulder returns to the X-Files office he turns the calendar all the way to November. Since Scully is returned the next episode after this, she must have been missing for at least 3 months, not 1.
- Mulder is seen following Dr. Calderon to a mansion-like building where Calderon is killed by two shape-shifting men. As Mulder is about to enter the building, one of the shape-shifters is now in the form of Calderon and leaving the building, Mulder decides to follow him. Later we see Mulder return to the same building and we find out it is a nursing home. After Mulder talks to Anna Fugazzi, he explores the nursing home further and finds a room where several elderly women are getting their beauty sleep treatment. As he comes out of the room, Kresge tries to detain him but Calderon shows up. Mulder tries to convince Kresge that Calderon is the bad guy, but not to shoot him. Kresge shoots Calderon anyway and gets knocked out by the noxious, green gas. Mulder runs out of the building and calls 911 but he is unable to give a location. He tells the dispatcher, "I don't know where I am."
- At 6:12, the domed building shown with the caption "San Diego Hall of Justice" is actually the Pima County Courthouse in downtown Tucson, Arizona.
Cast and Characters
- Bob Morrisey (Dr. Vinet) previously played Dr. Simon Bruin in The X-Files episode "Teliko" and Charles Cort in the Millennium episode "Blood Relatives."
- Sheila Paterson (Anna Fugazzi) previously played Gina Watkins in The X-Files episode "Fallen Angel."
- John Pyper-Ferguson as Detective John Kresge
- Sheila Larken as Margaret Scully
- Pat Skipper as William Scully, Jr.
- Karri Turner as Tara Scully
- Bob Morrisey as Dr. Vinet
- Gerard Plunkett as Dr. Ernest Calderon
- Patricia Dahlquist as Susan Chambliss
- Lauren Diewold as Emily Sim
- Tom Braidwood as Melvin Frohike
- Eric Breker as Dark Suited Man #1
- Stephen Mendel as Dark Suited Man #2
- Tanya Huse as Medical Technician