The Second Battle of Area 51 was a battle during the War of 2016.
The Earth Space Defense launched a failed counterattack on the Harvester Mothership in an attempt to kill the Alien Queen and neutralize the invasion, and satellite communications are destroyed. However, a discovery of a container from the wreckage of an unknown alien ship that was shot down on the Moon a day prior revealed an artificial intelligence that is part of a coalition of alien races that opposed the Harvesters and came to Earth to evacuate humanity. The A.I. revealed its utmost importance as the Harvesters are aware of its presence since its activation and the Sphere implored the ESD to destroy it before it can be capture by the Harvesters.
However, ESD Director David Levinson and scientist Brackish Okun saw another chance to eliminate the Queen: by using the Sphere as a decoy in order to lure the Queen into a trap. The ESD isolated the Sphere inside a chamber and duplicate its RF frequency into a transmitter on a space tug, which is loaded with cold fusion bombs, to lure the Queen into capturing the tug while the resulting explosion is contained with Area 51's shield generators. The pilot of the space tug, however, must sacrifice themselves in order to detonate the Queen's personal ship as it captures it. War hero Thomas Whitmore willingly volunteer to be the pilot.
Without modern telecommunication and radar, the ESD utilized Area 51's mothballed radar equipment to coordinate the operation.
The ESD implement their plan as the aliens began their assault on Area 51, as the base provides distraction for the main alien attack force. Whitmore lured the Queen's personal ship away from Area 51 to the salt flats where David Levinson oversee the shield generators. Incidentally, Julius Levinson drove a school bus of children to reunite with David.
The trap succeeded and the ship was instantly destroyed. However, the Queen survived the explosion due to being protected by a powerful energy shield built inside her suit. The Queen saw the Levinsons' group and began to chase them down as they fled on the school bus. Lieutenant Patricia Whitmore led a squadron in attacking the Queen and succeeded in destroying her personal shield despite sustaining the complete loss of her entire wing. Soon after, ESD pilots Dylan Hiller, Jake Morrison, Rain Lao, and Charles Miller arrive with hijacked alien fighter crafts and attack the shield-less Queen.
During this time, the attack on Area 51 allowed the base's alien prisoners to become free and notified the Queen of the Sphere's exact location. The Queen then telekinetically controlled her entire fighters (including the ESD pilots in their alien fighters) to protect her as she stormed to Area 51. The ESD pilots managed to break out of the swarm by overheating their crafts' fusion drives and were able to fatally wound the Queen just as she grabbed hold of the Sphere. After the Queen died from her wounds, the alien fighters lost all cohesion and began to fall from the skies and the Harvester Mothership ceased its operation and abandoned Earth.