Scully has called Mulder out to California to be a witness at her adoption hearing. He tells her the Frohike has hacked into the adoption records and found that Emily's mother of record is a woman named Anna Fugazzi, which he thinks is a fake name. Mulder is worried about her safety, considering the fate of Emily's foster parents, but tells the judge that Emily was conceived using ova taken during Scully's abduction. After finding Emily sick with a strange cyst on her neck, Emily is hospitalized. The cyst releases toxic green blood it is popped and Emily is promptly put into quarantine.
The doctor at the clinic where Emily was a patient refuses to transfer medical records, so Mulder roughs him up a bit and demands everything that's needed to make her better. Panicked, the doctor visits with the dark-suited men who murdered Emily's father parents. They kill him, revealing that he's an alien-human hybrid, and assume his identity. The hospital determines that Emily is suffering from some sort of tumorous growth. One of the dark-suited men injects Emily with something.
Mulder finds that there's an actual Anna Fugazzi, an elderly woman in a nursing home. Emily's condition declines as the tumor spreads. Mulder realizes that the women in the nursing home were being treated by the clinic doctor with the same kinds of hormones. He also finds medical records related to Scully and an alien fetus growing in a vial of green liquid. A local detective takes the evidence from Mulder as he tries to leave, then loses it to a dark-suited man, who manages to escape by taking the detective's identity.
Mulder and Scully sadly contemplate that Emily was made to serve an agenda, and never meant to be. Emily dies, and Mulder tells Scully that all evidence of the plot has been disposed of. Scully says that Emily's body is the last remaining evidence, but that too is gone, replaced by sandbags. Only Scully's cross necklace remains.
Episode Body Count
Dr. Calderon: neck-stabbed by the dark-suited men.
Emily Sim: dies after being injected with some sort of substance by a dark-suited man.
Cumulative Body Count (104/202 episodes, 0/2 movies)
Humans: 1,232Creatures: 82
Grand Total: 1,371