Three years after the events of the previous film, Commander Patrick Ross leads a manned mission 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.
Upon their return, Patrick and his team are told to refrain from sexual activity for ten days. Patrick disregards this advice and has a threesome with two sisters following a fundraiser. During sex with the second woman, he begins to sprout tentacles. The lady notices his transformation while she is stroking his body and is horrified at the sight of him whereupon she tries to free herself from his clutches. Both mothers experience accelerated pregnancies, culminating when Patrick’s half-alien children violently explode from their abdomens. Patrick hides both corpses and his rapidly growing sons on the property of his father, U.S. Senator Judson Ross. The next day, Patrick tells his father he cannot remember the previous night’s events. Senator Ross indicates that he is aware of Patrick’s behavior and tells him to focus on his political goals.
Dr. Orinsky, one of the NASA scientists who examined Patrick, discovers something amiss about his blood sample and desperately tries to contact Cromwell. However, Orinsky is ambushed and disemboweled by an alien Patrick, who snuck into the labs. Laura discovers that the DNA in Orinsky’s wounds is distinct from Eve’s, prompting Colonel Burgess, the military supervisor in charge of her project, to reunite her with Press Lennox to contain the new threat. Press and Laura seek out Cromwell, Orinsky’s former professor, and learn that he discovered that the alien species had attacked and destroyed Mars in ancient times. Because of his fears that alien DNA might remain on Mars to infect anyone who visited the planet in the future, Cromwell urged the government to abort the mission, but was institutionalized to permanently silence him.