On July 2, a massive alien mothership enters orbit around Earth and deploys saucer-shaped spacecraft 15 miles (24 km) in width that position themselves over major cities. In New York City, David Levinson (Jeff Goldblum) discovers transmissions that he believes the aliens use as a timer to coordinate their attack.
David and his father Julius (Judd Hirsch) warn the President, Thomas J. Whitmore (Bill Pullman), of the attack by playing on David's relationship with his ex-wife Constance (Margaret Colin) who is on the President's staff. The President orders evacuations of the targeted cities shortly before the aliens' timer runs out. The President, his daughter, portions of his staff and the Levinsons narrowly escape aboard Air Force One as the destroyers lay waste to Washington, D.C, New York City, Los Angeles and other major cities around the world. The President's wife, First Lady Marilyn Whitmore (Mary McDonnell), was at a speaking engagement in Los Angeles and was evacuated, but the helicopter crashes.
Captain Steven Hiller (Will Smith) is at his girlfriend Jasmine's (Vivica A. Fox) home for the holiday weekend when he is recalled due to the emergency. Leaving Jasmine and her son, he joins the attack against the aliens and asks her to meet him at the base. Russell Casse (Randy Quaid) is a former pilot from the Vietnam War believed to be suffering from posttraumatic stress disorder after claiming to have been abducted ten years earlier in the war by aliens. According the Russell, these are the same aliens currently attacking Earth. Russell and his children drive through the desert with a caravan of like-minded people in trailers in an effort to escape the populated city centers.
On July 3, the United States counterattacks; the Black Knights, a squadron of Marine Corps F/A-18 Hornets, attack a destroyer near the remains of Los Angeles. Their weapons fail to penetrate the craft's force field, and it releases scores of smaller "attacker" ships which are armed with similar shields and weaponry; a one-sided dogfight ensues. Hiller survives by luring an attacker to the Grand Canyon,[4] where he causes it to crash and then subdues the alien pilot. Hiller is picked up by Russell Casse. They take the captured alien to Area 51, where the President and his staff have landed. Area 51 conceals a top secret facility housing a repaired attacker and three alien bodies recovered from Roswell in 1947.
Jasmine and her son stumble upon the First Lady who is severely wounded from the helicopter crash and care for her along with other refugees. They make their way to the base only to find it destroyed by the attackers. Hiller steals a helicopter and goes to the base where he reunites with Jasmine and her son.
The alien regains consciousness in the Area 51 lab, and reveals that its species travels from planet to planet, harvesting a planet's resources before moving on. The alien attempts a psychic attack against Whitmore, but is killed by secret service agents. Whitmore orders a nuclear attack on a destroyer. The mission is aborted when a nuclear missile fails to penetrate the alien's shield. The injuries to the First Lady prove to be fatal.
On July 4, David devises a plan to use the repaired attacker to gain access to the interior of the mothership in order to introduce a computer virus and plant a nuclear bomb. It is hoped that this will cause the shields of the Earth-based alien craft to fail long enough for a worldwide attack to eliminate them. Hiller volunteers to be the mission's pilot, with David accompanying him to upload the virus. Hiller and Jasmine are married with David and Constance as witnesses. With few pilots to man available aircraft, the battle requires volunteers, including Whitmore and Russell, who have previous combat flight experience. Morse code is used to contact armies around the world in order to coordinate the attack without raising the aliens' suspicions.
After the virus is implanted, Whitmore leads an attack against a destroyer approaching Area 51. The fighters' supply of missiles are exhausted against the craft and its large complement of attackers, and the destroyer prepares to fire its main weapon at the base. Russell possesses the last remaining missile, but his firing mechanism jams. He pilots his aircraft into the center of the alien weapon in a suicide attack, annihilating the ship. Human forces all over the world bring down the remaining destroyers using the same method. Hiller and David, who have discovered the aliens preparing a large ground invasion force, are discovered aboard the mothership. They are unable to make their planned escape and release their missile into the center of the mothership. After releasing the weapon they manage to escape before the device detonates, destroying the mothership. Hiller and David return to earth unharmed, crash-landing their ship near Area 51. The world celebrates, and the main characters watch debris from the mothership enter the atmosphere.