After the arrival of the City Destroyers on July 2 and the mass destruction of human cities, alien forces were unimpeded in their systematic campaign of wiping out human infrastructure. Human military forces were unable to stop the Harvesters due to their deflector shields that made their vessels completely invulnerable to conventional weapons, including nuclear weapons.
However, on the morning of July 4 1996, David Levinson, an MIT-trained satellite technician assigned to work with Area 51's research staff, inadvertently discovered a way to deactivate the Harvesters' shields. When the alien mothership first arrived to Earth, the alien ship from the Roswell incident that was in Area 51's possession reactivated and allowing the facility's scientists in gaining new insights into the alien technology. Through his work with Area 51's staff, his studies of the aliens' communications signal, and inspired by his father Julius Levinson, David realized that the aliens drew all of their coordination and energy from the mothership in orbit, which he could transmit a coded virus into the mothership's systems, allowing it to filter into all of their vessels and shutting down their shields. This would allow human conventional weapons to temporarily strike back at the invaders before they discover the virus. However, this plan requires directly infiltrating the mothership. David proposed using the captured alien ship to gain entry, and as well deploying a nuclear warhead to cripple the mothership after the virus was uploaded and thus ensure disorientation amongst alien forces on Earth.
U.S. President Thomas Whitmore approved of Levinson's plan and contacted every military forces on Earth through Morse code to organize a united counteroffensive. In which American forces will lead the first attack to confirm the shields are disable before relaying the news to their allies. Forces in Europe, the Middle East, and Asia were able to confirm their readiness.
USMC Captain Steven Hiller volunteered to pilot the captured spaceship with David Levinson to personally upload the virus. Upon entering the mothership, alien forces inside the massive vessel were being prepared for a ground invasion of Earth once the City Destroyers have completed their task. Levinson was able to upload the virus; however, he and Hiller were unable to escape after their ship was permanently docked, forcing them to hide from the aliens throughout the duration of the counterattack.
On Earth, President Whitmore led a strike force composed of available military pilots and volunteers against a City Destroyer approaching Area 51. Whitmore's attack confirmed Levinson's virus had worked and allowing all human forces to mounting their counterattack. It is during the battle at Area 51 that the Americans learned that the City Destroyer's weakness is their primary weapon and that destroying it will cause a explosive backlash that completely destroys the ship. Soon afterwards, the Americans notified of the Destroyers’ weakness to the other military forces on Earth.
After Whitmore's forces destroyed the City Destroyer, Levinson and Hiller resigned to their fate that they will not escape but decided to launch the nuclear warhead. To their surprise, after launching the warhead which destroyed a observation room, it caused their ship to come loose. The two made a harrowing escape from the mothership before it is subsequently vaporized in a massive explosion. Levinson and Hiller safely returned to Earth and landed their ship in the outskirts of Area 51. With the mothership destroyed, the City Destroyers on Earth were severely weakened and brought down by human forces.