During the SETI program, Earth's scientists send out transmissions with information about Earth and its inhabitants, DNA structure, etc., in hopes of finding life beyond Earth. They then receive transmissions from an alien source on how to create endless fuel effortlessly. Therefore, the scientists assume that this is a friendly alien species. From a second alien transmission, the scientists receive information about an alien DNA along with instructions on how to splice it with human DNA. A government team led by Xavier Fitch goes forward with the genetic experiment attempting to induce a female, under the assumption that a female would have "more docile and controllable" traits.
Three years after the events of the Species (film), Commander Patrick Ross leads a Human mission to Mars to Mars. Soil samples collected by Patrick's team of astronauts unwittingly contain an extraterrestrial substance which thaws aboard their capsule due to the temperature difference and contaminates them, causing a seven-minute contact gap with mission control. With seemingly no subsequent negative effects, the astronauts return to Earth to public celebration. Only an institutionalized former scientist, Dr. Cromwell, reacts to their return with violent panic. Meanwhile, Dr. Laura Baker has created a clone of Sil named Eve, whose alien DNA is suppressed to make her more docile. Her team conducts experiments on Eve, hoping to find a way to combat the alien species should it ever return to Earth. Every experiment is unsuccessful as Eve's biology adapts.
Hours after the events of the Species II, 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 gunpoint. They are ambushed by the "half-breed" alien child hiding in the van, who kills the co-driver with his tongue. The driver discovers both the half-breed and a reviving Eve in the back of the van; the half-breed strangles Eve to death while she gives birth to a newborn alien, which the driver flees with. Government agent Wasach orders an autopsy, discovering Eve's pregnancy, then has her body burned.
When she reaches the end of her lifespan, a scientist rushes to Mexico, in order to save the half-breed alien seductress he raised as his docile niece, but soon awakens the deadly, sexual predator inside her.