“Emily” is episode seven of season five of The X-Files.
In the previous episode, “Christmas Carol”, Scully had discovered that Melissa wasn’t Emily’s mother – Scully was. This episode opens with Scully narrating as she walks barefoot through the sand. She finds the necklace she gave to Emily and picks it up, before turning to sand and blowing away.
Mulder arrives at the San Diego County Children’s Centre. He asks for the special needs ward, and finds Scully with Emily. Scully asks Mulder if something’s wrong; he says he’s found Emily’s surrogate mother. Frohike hacked into the California Social Services adoption database and found an Anna Fugazzi is the mother of record. Fugazzi is a slang term for fake. There are no true records as Emily didn’t come into the world through any system that keeps them. She was born through someone who will do anything to protect Emily and their interests. Scully will protect Emily, but Mulder asks who will protect her. Emily’s adoptive parents are both dead, and not by accident.
Scully believes there’s only one right thing to do and didn’t call Mulder earlier because she couldn’t believe it. She needs him now as a witness on her behalf at her hearing. Mulder thinks he should have declined, if he ever wanted to see Scully free from harm. He knows something they will use against her that could jeopardise her custody of Emily. Emily is a miracle that was never meant to be.
At the hearing, Mulder testifies to the judge that Scully was abducted by an agent of the federal government, along with 12 other women. She was missing for four weeks, during which all her ova were extracted. The judge asks can that be done. Mulder says it can and was; he sees no other way of explaining it. A medical examination of Scully will show she never gave birth. The judge wants an explanation. Mulder doesn’t have one, but Scully is Emily’s mother. Not by legal definition, according to the judge. Mulder would like to see a legal precedent for this situation. Scully is trying to adopt her own flesh and blood and they have no right to question or to stand in the way.
That night, at her brother’s, Scully asks why Mulder didn’t tell her about her ova. He never expected to have to and thought he was protecting her. The phone rings during their conversation, but there’s no-one on the other end. Mulder has it traced and it leads to the children’s centre. They head there and find Emily. Mulder says she’s burning up, then discovers a green-tinged cyst on her neck.
The staff doctor says Emily is running a fever; she has an infection probably related to the cyst. They’re going to have it biopsied. He asks Scully about Emily’s history, and she mentions the experimental treatment for anaemia she was being given. The other doctor is about to biopsy Emily when Mulder suddenly tells her to stop. She doesn’t and the green liquid seen before comes out of the cyst and the doctor is affected.
Emily is taken to a quarantine ward and Mulder says the other doctor is in and out of consciousness. Scully asks how he knew. If Emily is a creation, then she could have the same biochemistry they’ve seen before. The doctor has been treated the same way Scully treated Mulder when he was affected.
Scully is told that Dr Calderon refuses to transfer Emily’s medical records. Scully states Calderon is endangering Emily’s life; apparently, he is claiming the same of Scully. Emily is in a double-blind medical trial and Scully has no authority over her.
Mulder heads to see Calderon at Prangen Pharmaceuticals. Calderon is not helpful; he can’t release information on experimental drug trials. It would expose them to litigation and they need to protect their research. Mulder attacks Calderon and points his gun in his face, leaving when security comes. He then follows Calderon when he leaves. Calderon heads to a house where the two men seen with, and who probably killed, Emily’s adoptive father, are waiting. They are not happy he brought Mulder to them. One kills him using the tool used by the alien bounty hunter, then both change their faces to match Calderon.
Emily’s condition is deteriorating. An MRI scan shows something growing insider her. Not cancer, but it is killing her. Mulder, meanwhile, is looking into Emily’s birth and, it turns out, that of a few other children too.