Confused by this, Mulder finally confesses to Scully that when women are abducted(as was she in the Duane Barry/Ascension arc), their eggs are taken and clones, alien/human children, are created. Scully learns that Emily's adoptive mom wanted to stop the tests that were being done on her daughter, and that is why she was murdered. Before Marshal Sim can be released, he also dies.
Scully wishes to adopt Emily, but the state does not wish to give her custody because of her job. Scully realizes that Emily is a "unique" child and as much as she loves Emily, Scully cannot change her fate; the little girl dies from her illness.
Personal Info: Emily Christine Sim was born November 2nd, 1994. She was adopted by Marshal and Roberta Sim. Her surrogant mother was Anna Fugazzi, and her biological mother was Dana Scully. Biological father unknown; suggested to be extraterristial.
Siblings: In the episode Emily, Mulder found a fetus that had been created and was inside a container of green liquid. That fetus had Scully's name on it. Because all of the womens' eggs are taken, an abducted woman can have many children. These siblings, X-Philes don't know names for, but Scully did give Emily one sibling that was not created like Emily had been; this was her half-brother, William.