When Earth comes under attack from an advanced extraterrestrial species, the survivors must band together to repel the invaders. On July 2, an alien mothership enters orbit around Earth, deploying several dozen smaller spacecraft to hover over many of the world's major cities. Satellite transmissions from the craft are discovered, by scientist David Levinson (Goldblum), to be a timer which he believes is a countdown to a coordinated attack by the aliens. Having made his way to the White House with his father, he warns President Thomas J. Whitmore (Pullman) of the impending attack. After three US Air Force helicopters are shot down by an alien spacecraft while attempting to establish communications, the president orders the evacuation of affected cities. Before the countdown reaches zero, he flees the White House aboard Air Force One with his staff and Levinson. At zero point, the hovering alien spacecraft open fire upon their targets with advanced directed-energy weapons, destroying entire cities and killing millions.
The United States counterattack is coordinated from El Toro and sees the alien spacecraft assaulted by Marine Corps fighter aircraft. The attacks are useless, as both the larger craft and individual fighters launched from within are protected by seemingly-impenetrable force fields. While leading his unit of fighter pilots in an attack against the aliens, Captain Steven Hiller (Smith) is involved in a dogfight with an alien fighter which sees both crash in the desert. Having parachuted to safety, Hiller subdues and captures the injured alien. As the El Toro airbase has since been destroyed, Hiller takes the alien in the direction of the nearby Area 51 base, where the president and his remaining staff have also landed. There, they discover a top secret facility housing a captured alien fighter and three alien bodies recovered from Roswell in 1947.
When lead scientist Dr. Brackish Okun (Spiner) examines the new alien specimen, it attempts escape and takes control of his mind. When questioned by President Whitmore, through a telepathic connection it reveals that its species travels from planet to planet, destroying all life and harvesting the planet's natural resources, before moving on to the next conquest. The alien attempts a psychic attack against Whitmore and is killed by military personnel. Whitmore orders a nuclear attack on one of the larger alien spacecraft which is hovering over a by-now-evacuated Houston, but as the craft is still protected by its force shield, the attack fails.
Levinson devises a plan to gain access to the interior of the alien mothership in space in order to introduce a computer virus and plant a nuclear device on board. This, it is hoped, will cause the shields of the Earth-based alien craft to fail long enough for the human resistance to destroy them. Hiller volunteers to fly the captured alien fighter and Levinson accompanies him to upload the virus. With satellite communications knocked out, the Americans use morse code to coordinate an attack with the remaining air forces around the world, timed to occur when the invaders' shields are set to fail.
With the successful implantation of the virus, President Whitmore leads the US fighter jets against an alien spacecraft on approach to Area 51. The attack is initially unsuccessful and the fighters soon exhaust their supply of missiles. The underside of the alien craft opens up as its primary weapon of mass destruction is prepared to fire on the base. Russell Casse (Quaid) finds that he possesses the one remaining missile. The firing mechanism damaged, he pilots his jet into the opening in a kamikaze attack. The ensuing explosion causes a chain reaction which destroys the alien spacecraft. Human resistance forces around the world use the same weak point to destroy the remainder of the alien ships, while the nuclear device planted by Hiller and Levinson destroys the alien mothership. Hiller and Levinson escape unharmed, crash-landing their captured alien fighter in the desert close to Area 51.
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