On July 2, 1996, an enormous mothership orbits around Earth, deploying assault fortress saucers, each with a fifteen-mile radius, that take positions over Earth's major cities. David Levinson, an MIT-trained satellite technician, decodes a signal embedded within global satellite transmissions, realizing it is the aliens' countdown timer for a coordinated attack. With help from his ex-wife, White House Communications Director Constance Spano, David and his father Julius gain access to the Oval Office and alert President Thomas Whitmore to the threat. Whitmore orders evacuations of New York City, Los Angeles, and Washington, D.C., but it is too late. The saucers fire destructive beams, causing massive explosions that kill millions. Whitmore, the Levinsons, and a few others narrowly escape aboard Air Force One as the capital is destroyed, along with the other locations over which the city-destroying warships are positioned.
On July 3, counterattacks against the alien invaders begin worldwide, but their warships are shielded by force fields. Each saucer launches a swarm of attack fighters with their own shields as well, which decimate the human fighter squadrons and military bases. Captain Steven Hiller, one of the mission's squadron leaders with the United States Marine Corps based out of El Toro, survives by luring his attacker to the enclosed spaces of the Grand Canyon before ejecting from his plane safely, causing the enemy fighter to crash-land. He subdues the downed alien and flags down a convoy of refugees, hitching a ride with former combat pilot Russell Casse. They transport the unconscious alien to Area 51, where Whitmore's group has landed. Secretary of Defense Albert Nimzicki has revealed that a faction of the government has been involved in a UFO conspiracy since 1947, when one of the invaders' attack fighters crashed in Roswell. Area 51 houses the now-refurbished alien fighter, and three alien corpses recovered from the crash. As scientist Dr. Brackish Okun examines the alien captured by Steven, it regains consciousness and attacks, telepathically invading Okun's mind and killing other personnel. It uses Okun's vocal cords to communicate before launching a psychic attack against Whitmore. After Secret Service agents and military personnel kill the alien, Whitmore reveals what he learned when they were linked: the invaders plan to strip Earth of natural resources. He reluctantly authorizes a nuclear attack against one warship situated above Houston as a trial, but it remains intact. Meanwhile, Steven's fiancée Jasmine Dubrow and her son, having survived the destruction of Los Angeles, rescue other survivors, including the critically injured First Lady, Marilyn. Though they are later found by Steven and taken to Area 51, Marilyn dies shortly after being reunited with her family.
On July 4, David writes a computer virus as a means to deactivate the aliens' shields, and devises a plan to do this by uploading it into the mothership from the refurbished alien fighter, which Steven volunteers to pilot. The U.S. military contacts surviving airborne squadrons around the world through Morse code to organize a united counter-offense against the aliens. With military pilots in short supply, Whitmore enlists the help of volunteers with flight experience, including Russell, to fly the remaining jets at Area 51; and leads an attack on a warship bearing down on the base. Entering the mothership, Steven and David upload the virus and deploy a nuclear missile on board, nullifying the aliens' communications system and reinforcements followed by its obliteration. With the aliens' shields deactivated, Whitmore's squadron is able to combat the enemy fighters, but their ammunition is exhausted before they can destroy the saucer. As it prepares to fire on the base, Russell has one last missile, but is unable to fire due to a launcher malfunction; he sacrifices his own life by crashing his jet with the missile into the saucer's weapon, which destroys the warship completely. Human military forces worldwide are notified of the alien ships' critical point and successfully destroy the others. As humanity is rejoicing in victory, Steven and David return to Area 51 unharmed and reunite with their families.
