University of Wisconsin graduate student Teri MacDonald, Helen Hunt, has trained a chimpanzee named Virgil to use sign language. When her National Science Foundation grant isn’t renewed, she is forced to sell Virgil. He is taken to an Air Force base in Lockridge, Florida, to participate in a top-secret flight-simulation project, though officials insist he has been sent to the Houston Zoo. The situation sets up a tense clash between scientific curiosity, military secrecy, and the fate of a highly intelligent animal.
Airman Jimmy Garrett, Matthew Broderick, is assigned to the same project. Jimmy and Virgil quickly form a bond, and Jimmy learns that the chimpanzee can sign. Unbeknownst to him, once the chimps reach a certain level of operation in the flight simulator, they will be exposed to a lethal pulse of radiation to determine how long a pilot may survive after a nuclear exchange in a second-strike scenario. The ethical implications of the experiment begin to weigh on Jimmy, even as the base staff push forward with the dangerous tests.
When Jimmy becomes aware of the deception, he contacts Teri and arrives at the base to weigh his options. Teri arrives with news that she will inform the NSF, but time is not on their side because Virgil’s life hinges on the schedule. Jimmy challenges Dr. Carroll and others about the project’s value, arguing that a hypothetical pilot, aware of the second-strike implications, would be aware that he is dying, and thus his mental state would be altered—whereas the chimpanzees would not share that awareness, rendering the experiment fundamentally flawed. Enraged, Dr. Carroll warns that Jimmy’s military career would be finished if he continues to press the issue.
Meanwhile, back in the vivarium, several chimpanzees have unlocked their cages and stacked crates and boxes to attempt an escape through a skylight. Jimmy, Teri, Dr. Carroll and the authorities walk into the vivarium to find the chimps loose. Virgil is at the top of the stack and tries to break the skylight with a crowbar, but Teri urges him to come down. Dr. Carroll attempts to corral the chimps with an electric prod, yet Goliath—the strongest among them—overpowers Carroll and the others, forcing the humans to flee. The chaos spreads as many chimpanzees break free and run amok across the base, while Goliath, Winston, and Spike reach the flight chamber with dangerous intent.
Inside the chamber, Goliath and the other two chimpanzees wreak havoc, damaging the simulator and shorting the wall control panel of the reactor, triggering a dangerous radiation release. Jimmy, Teri, and Virgil arrive just as the chimps continue to sabotage the chamber. Jimmy manages to pull Winston and Spike to safety, escaping by a hair’s breadth, but Goliath refuses to leave and becomes trapped in the flight chamber as the reactor’s panel short-circuits and a radiation blast looms. A fire extinguisher left by the chimps jams the reactor, creating a risk of meltdown—yet Jimmy and Virgil persuade Goliath to yank out the jammed extinguisher, averting disaster, though Goliath later succumbs to radiation exposure.
In a bid to help the chimpanzees escape, Jimmy and Teri steal a military plane, but they are stopped by the military police. While the officers hold them, Virgil takes the controls and pilots the plane, guiding the chimps to safety as they fly away. The aircraft eventually crashes in the nearby Everglades, and a search party is cautiously called off as the field goes quiet. In a final quiet moment, Jimmy and Teri spot Virgil hidden in the brush with his chimpanzee mate Ginger. Teri signs to Virgil that he and the others are now “free,” and the chimpanzees melt back into the vast, green expanse of the Everglades.
