The film begins immediately where Species II left off. Hours after the events of the previous film, the medical van transporting the lifeless Eve has lost its way, but when the co-driver tries to radio their superiors, the driver stops and holds him at gun-point. Both are surprised by the alien child (now called “half-breed”) appearing in the back window and killing the co-driver with his tongue. In the back the driver finds the half-breed and a reviving Eve, who goes into labor and gives birth to a new-born alien. While the half-breed strangles Eve with his tongue, the driver wraps the new-born in his jacket and runs off through the forest as a military helicopter finds the deserted van. Government agent Wasach orders an autopsy and afterwards the burning of Eve’s body. The driver is revealed as Dr. Abbot, teaching biochemistry at a university, who believes it is wrong to decide whether a species should live or die. In his home, he keeps Eve’s offspring, who within a few months has grown into a young girl named Sara. The half-breed that killed Eve visits Dr. Abbot in his office, asking to see “it” (Eve’s offspring), but then partly decays and dies in his chair. The shocked Doctor asks Dean, a student whose funding is in jeopardy, to assist him in his research to create a perfect alien DNA, promising him funding and future awards. In Abbot’s absence, Sara undergoes a metamorphosis similar to Sil’s that envelopes her into a cocoon, destroying her clothes, but transforming her into a beautiful blonde young woman. When Dr. Turner, a fellow professor, arrives at Abbot’s house, he comes across Sara, who is naked, and tries to seduce him, but when he comes near her she rejects him when she detects that his genes are imperfect. Dr. Turner, annoyed at his lost opportunity, implies to Sara his intention to rape her and tries to but is killed by Sara. Looking for prospective breeding partners, Sara strolls onto campus (clothed), and finally makes contact with another half-breed, who’s on a train that accidentally injures Sara while she was running after it. A woman, who picked her up, watches in horror as Sara’s arm starts to regenerate. The two begin to mate but Sara rejects him when she discovers that he suffers from diseases. Earlier, Sara had an encounter with Dean in Abbot’s home, wondering if she can trust him. Later on, at Abbot’s house, the angry half-breed attacks Sara and tries to impregnate her. Abbot sprays hydrochloric gas over the lab, killing the half-breed, but not before it fatally wounds him. Before dying, Abbot begs Dean to continue his work. Left in charge, Dean ponders whether he should continue alone. Sara urges him to save her species. Later, Dean follows Sara to his campus, where he encounters her in a classroom. She tries to have sex with him, but he sees her in her alien form and resists. Meanwhile, Dean’s campus roommate, Hastings, contacted a website, on which a woman called Amelia wants to date biochemists, feeding her data from Dean’s notes. Amelia, the leader of the half-breeds, responds to it and begins to arrive at his campus. On her way she stops at a gas station, where a gas attendant seeing her body naked, decides to rape her. She allows him to rape her before killing him. She then arrives at the campus and is looking for Eve’s offspring. She senses Sara’s presence and kidnaps Hastings. At Abbot’s house, Amelia and Sara pressure Hastings into creating the perfect species so that both can have mates. Dean is picked up by agent Wasach, who also monitored the Amelia website and observed some connection to the disbanded project Athena. The two interrupt the proceedings at Abbot’s house and take Sara’s harvested eggs. The three humans flee to a nearby experimental power plant, followed by Amelia and Sara. Dean attempts to trap Sara and Amelia in the plant’s core. When Sara’s eggs fall into the core, Amelia attempts to kill Dean, and kisses him but is stopped by Sara, who throws Amelia into the core. Dean manages to close the shaft to the core just in time to prevent a nuclear disaster, but not before Sara also falls down the shaft. Later, when Hastings drops by Abbot’s house, he finds Sara alive, along with a new alien boy. Dean explains that he pulled Sara to safety and created the perfect mate for her, using the salvageable parts of the half-breed DNA so that Sara wouldn’t be alone. Dean asks Sara why she saved him, since with her eggs gone there was no reason to. Sara doesn’t answer, but it’s indicated that she’s grown to care for Dean. After Sara and her mate have departed, Dean reveals to Hastings that he ensured the mate would be sterile, thereby preventing any offspring.
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