On July 2, a giant alien mothership, over 340 miles in diameter (550 km) enters orbit around Earth and deploys several dozen saucer-shaped "destroyer" spacecraft, each 15 miles (24 km) in width. The destroyers take positions over many of Earth's major cities, including New York, Washington, D.C. and Los Angeles. David Levinson (Jeff Goldblum), an MIT-graduate working for a cable company in New York City, discovers hidden satellite transmissions which he believes is a timer counting down to a coordinated attack by the aliens. With the help of his ex-wife Constance Spano (Margaret Colin), a White House staffer, David and his father Julius (Judd Hirsch) gain entrance into the Oval Office to warn President Thomas J. Whitmore (Bill Pullman) of the impending attack. The President immediately orders large-scale evacuations of the targeted U.S. cities, but the aliens attack with advanced directed energy weapons before the evacuations could be completed. The President, his young daughter, portions of his staff, Constance and the Levinsons narrowly escape aboard Air Force One as a destroyer lays waste to Washington D.C.
On July 3, the United States conducts a coordinated counterattack; the movie follows the Black Knights, a squadron of Marine Corps F/A-18 Hornets from El Toro Marine Corps Air Station, as they participate in an assault on the destroyer that has devastated the city of Los Angeles. Their weapons fail to penetrate the craft's force field, and it responds by releasing scores of smaller "attacker" ships which are similarly shielded and armed with high-energy torpedoes. One-sided dogfights ensue. Captain Steven Hiller (Will Smith) manages to evade the guns of the attacker ships and lures a single attacker to the Grand Canyon. There, as his jet is about out of fuel and the attacker is about to overtake him, he deploys the landing chute for his jet and it drapes across the alien craft, temporarily disorienting the pilot. Captain Hiller then ejects from his jet. The alien crashes into the top of the canyon wall and lands in the desert. Captain Hiller parachutes to a landing close by and angrily marches over to find and confront whatever life form is in the alien craft. The door to the alien fighter craft pops open and a very bizarre looking creature with tentacles appears. Captain Hiller delivers a right cross and knocks the creature out, saying "Welcome to Earth!!" He sits down and smokes a victory cigar.