The ambulance carrying Eve, Natasha Henstridge, the corpse of a key subject, goes off course and loses its way. When the co-driver tries to radio in, the driver, Dr. Abbot, Robert Knepper, pivots suddenly and holds him at gunpoint. The vehicle is then ambushed by Portus, who kills the co-driver with a cruel, almost serpentine tongue. In a shocking turn, Abbot discovers Portus and Eve alive in the back, and Portus strangles Eve to death while she gives birth to a newborn alien—an event Abbot escapes with, clutching the infant. Government agent Wasach orders an autopsy once he learns of Eve’s pregnancy, and then orders the burning of Eve’s body.
Abbot returns to his ordinary life teaching biochemistry at a university and begins to raise Eve’s child, Sara. Sara grows from a child into a young girl under his care, a life shaped by the strange events that linked her to Eve’s legacy. One night, Portus, who has aged dramatically and fallen critically ill, visits Abbot’s office. Abbot attempts to treat him, but Portus insists on seeing Sara and reveals that there are other half-breeds suffering from similar afflictions. Portus dies in Abbot’s chair, marking a grim turning point in the tale. Meanwhile, Dean, one of Abbot’s students, finds himself facing jeopardized funding for an experimental power plant project. Abbot presses Dean to help perfect the alien DNA to save the species, offering him a share of any funding or awards their work might win in return.
In Abbot’s absence, Sara cocoons herself and then emerges as an adult. Abbot’s superior, Dr. Turner, Christopher Neame, arrives at the house seeking Abbot and encounters Sara. She initially tries to seduce Turner but quickly rejects him; Turner then attempts to rape her, and she kills him before setting out to find a mate. Abbot returns home, finds evidence of Sara’s transformation, and disposes of Turner’s body. Sara eventually connects with another half-breed but discovers his illnesses and, in a fit of ferocity, knocks his tooth out. Abbot and Dean continue their experiments on Sara, and Abbot explains the government’s Project Athena, which previously created Sil, and Sara’s lineage as the child of Patrick Ross infected with Martian alien DNA from Eve—Sil’s clone. The half-breed Sara rejected earlier breaks into the lab, mortally wounds Abbot, and attempts to impregnate her, only to be killed by hydrochloric gas Abbot releases.
Dean weighs whether to carry on Abbot’s work, and Sara urges him to save her species. Hastings, Dean’s roommate and a student, discovers Amelia’s dating website and passes Dean’s notes to Amelia after snooping through his research. Amelia, a fellow half-breed, agrees to meet. On the way, Amelia has sex with and murders a gas-station attendant who tries to rape her. At the campus, Amelia senses Sara and kidnaps Hastings, taking him back to Abbot’s home. Amelia and Sara force Hastings to help them refine the alien DNA using Sara’s purer biology to save the half-breeds and create suitable mating partners. Wasach, whose team had been monitoring Amelia’s website, tracks the connection to Project Athena and helps secure Hastings.
The trio—Dean, Hastings, and Wasach—flee to Dean’s experimental power plant with Sara and Amelia in pursuit. They attempt to trap Amelia and Sara in the plant’s core, risking a catastrophic meltdown. Dean drops the eggs into the core, and Amelia advances to kill him; Sara meanwhile attacks and hurls Amelia into the core. The trio manages to close the core in time to avert disaster.
In the aftermath, Hastings visits Dean at Abbot’s home and discovers both Sara and a half-breed alien boy. Dean reveals that he saved Sara before sealing the plant’s core, subsequently completing the refined alien DNA to produce a mate for her so she would not be alone. Once the boy matures, Dean tells Sara that she is on her own and to be careful. He also reassures Hastings that Sara’s mate would be sterile to prevent further reproduction, a safeguard for a fragile future.
