A rumored landing of a flying saucer in rural Iowa triggers a high-stakes investigation led by Andrew Nivens, Donald Sutherland, who runs a secret CIA unit tasked with studying extraterrestrial activity. He sends two agents to the crash site, but when they disappear, he travels there in person, joined by Sam Nivens, [Eric Thal], and Jarvis, [Richard Belzer], along with Dr. Mary Sefton, [Julie Warner], a NASA specialist, and their fellow field leader Alex Holland, [Keith David]. What begins as a routine inquiry quickly twists into a tense confrontation with locals who seem to display no genuine emotion, turning the crash site into a chilly, staged spectacle.
At the heart of the investigation, Mary tests the locals’ reactions during a meeting with a TV station manager, casually testing for a response by exposing herself, only to find the manager unmoved and uninterested. Suspecting that the man is not who he seems, Sam tries to take him into custody, but a brutal fight erupts in the man’s office, ending with the manager dead. The team discovers a slug-like alien attached to the man’s back, and they manage to capture it, initiating a chase as infected townspeople push back against their efforts. They retreat to their plane, but the aliens begin to spread across the town with alarming speed.
Back at their briefing, Sam notices that Jarvis has stopped chain-smoking, a telltale sign that something has changed. Suspecting infection, Sam and the team restrain Jarvis, only to find him unconscious and without the alien clinging to his back. In response, Andrew orders all staff to strip to test for infection, an escalation that includes his personal secretary Miss Haines, [Donna Garrett], who refuses to remove her shirt and tries to flee the building. The pursuit ends with a brutal confrontation in the office kitchen, where Sam and Alex Holland locate Sam and the now-dead secretary. Sam reveals to his father that the alien had gotten away, but the truth is far more chilling: Sam is already infected.
Jarvis, overwhelmed by withdrawal, commits suicide. The parasite-infected Sam visits Jarvis’s apartment and, with the help of the unsuspecting manager Greenberg, [Nicholas Cascone], opens crates of parasites Jarvis had shipped. Sam infects Greenberg, who, after removing his glasses, becomes a conduit for the aliens as they communicate telepathically and coordinate their spread. The aliens’ ability to “fix” ailments is revealed, and they begin to move toward a political center where the President plans to convene a meeting. The team realizes the threat is global as the President’s security detail becomes infected, but a dedicated tactical unit manages to intervene and save the President.
As Sam and Mary race to contain the threat, Greenberg departs with all the knowledge gained from those who have been infected. The infected force is interrogated back at the office, where they learn that the aliens control their hosts completely, including killing and reviving them. An attempt to shock the infected host reveals a weakness: electric shocks can briefly disrupt the alien control, though they injure the host. The alien warns that Sam will be killed to prove its power, and Mary administers massive electrical shocks to Sam, forcing the parasite to leave his body. Sam is resuscitated, but he endures a heavy withdrawal and leans on Mary for comfort as they begin to build a fragile trust.
Andrew pushes for a full-scale military intervention to eradicate the aliens, who have now spread across the entire region, infiltrating law enforcement and the Iowa National Guard. The aliens reproduce asexually by division, and their influence grows ever stronger. Mary and Sam uncover a chilling revelation: Mary herself has been infected by an alien that had infected Sam, and the aliens now know everything the humans know. To survive, they must avoid harming Mary, who remains a potential host.
Mary feigns a desperate escape and makes a perilous jump from Sam’s third-floor apartment into a car driven by Greenberg, while the infected masses move closer to a decisive confrontation. In Des Moines, two chimpanzees infected for research spread the parasite to a third, who types a hopeful message to Sam on a computer, confirming that the aliens share their collective knowledge. Sam and Alex deduce that the hive is carried by a massive river system and decide to infiltrate the hive in Des Moines using a transmitter Graves created that mimics the aliens’ communications frequency.
Inside the hive, Sam experiences persistent telepathic contact that nearly tempts him to surrender to the infection again, but he resists and opens fire on the infected. He finds Mary and, with the help of a rescued child kept in isolation from the infected crowd, they begin to flee. Alex enters the hive to aid them but comes under heavy fire, falling into a containment pool where the aliens reproduce. He pleads with Sam to leave him, but the parasite reasserts control, and Mary shoots and kills Alex to prevent further reinfection.
Sam, Mary, and the child reach the extraction point and are flown back to base. There, the team discovers that the isolated child once suffered from encephalitis, a vulnerability the aliens cannot overcome. They test the theory by infecting an alien with the encephalitis virus, which causes the creature to explode and die. A final outbreak of destruction seems contained, but a last alien clings to Andrew, revealed when he walks normally again after a cane-walk injury. Sam pursues his infected father to a helicopter showdown, where he finally shoots him, forcing the alien to depart. The tail rotor ends the parasite’s life, and Andrew, though wounded, acknowledges the depth of Sam and Mary’s bond and their growing relationship.
In the aftermath, Andrew confirms that the last alien is down and reflects on the extent of Sam’s love. With the danger seemingly over, Sam and Mary face an uncertain future but comfort one another with the knowledge that they have time to truly get to know each other—an uneasy, fragile hope against a memory of a threat that forever altered their world.
