As seen in Episode 5X05, Scully has learned she is the biological mother of three-year-old Emily Sim. Scully experiences a nightmare in which she discovers her gold cross lying on the ground as a sandstorm rages around her. Slowly, she, too, transforms into sand and dissolves into nothingness.

Mulder travels to the San Diego County Children's Center, where Scully is keeping an eye on Emily. Scully tells Mulder she needs him to be a witness on her behalf at a child custody hearing. Mulder informs his partner that Frohike accessed the California Social Services Adoption database. It turns out that Emily's mother of record is one Anna Fugazzi (a slang term for "fake"). He warns Scully that the men behind the conspiracy will do anything it takes to protect Emily-including jeopardizing Scully's custody of the girl. During the custody hearing, Mulder introduces a file documenting Scully's disappearance years earlier. He submits that Emily Sim was conceived through a scientific experiment. Despite this, he insists that Scully is nonetheless Emily's mother.

Scully receives another mysterious telephone call. A trace reveals its origin to be the County Children's Center. When the agents arrive at the scene, they discover a thick, fibrous cyst on the back of Emily's neck. As a doctor removes a biopsy sample from the cyst, it suddenly oozes green bubbling fluid. The doctor is overcome by the fumes and treated at the hospital. Afterward, Dr. Calderon refuses to transfer Emily's medical records to the Children's Center. An enraged Mulder physically assaults Calderon and warns that unless he produces the records, he can expect more of the same. Afterward, Calderon approaches the two dark-suited men at the Dimsdale Convalescent home. The men realize Mulder tailed Calderon to the building. They kill Calderon using an alien gimlet, then assume his form. One of the "Dr. Calderons" travels to the Children's Center and injects Emily with a greenish fluid. A surprised Scully chases "Calderon" through the hospital. But by the time she catches up to him, the alien has morphed into the form of a stranger. Mulder and Scully speak by phone. Mulder suspects the fluid injected into Emily will not cause her harm, as the conspirators want her alive... for reasons unknown.

Mulder makes his way inside the Dimsdale Retirement Home. There he discovers evidence that the elderly women residents-including Anna Fugazzi-were all given hormone injections. Frohike uncovers evidence that the elderly women all gave birth only a few years earlier.

Emily continues undergoing therapy and medical tests of all kinds, but her condition only deteriorates further. At one point she is placed inside a pressurized chamber. Suddenly, a snake-like creature stirs beneath her skin. Scully orders an end to the test. Mulder discovers cylinders containing live human embryos floating in a greenish fluid. He grabs three ampules of the greenish fluid and makes his way into a hallway. Detective Kresge suddenly steps forward, placing a gun to Mulder's head. Kresge removes the ampules from Mulder's hand. Suddenly, one of the "Calderons" appears at the end of the hallway. Mulder retrieves one of the ampules and runs off, warning Kresge not to fire on the advancing "Calderon." A confused Kresge shoots nonetheless, and is then overcome by noxious fumes. The alien "Calderon" then morphs into Kresge's form and makes his getaway.

Emily slips into a coma and dies. At the funeral, Scully tells Mulder there is still evidence of what the men did to Emily. But when she lifts the casket lid, she discovers several small sandbags inside (one has spilled its contents onto the bottom of the coffin). Scully retrieves her gold crucifix, the one she gave to Emily, from the sand.