This sequel sparks off twenty years after the events of the first film, during which the United Nations has collaborated to form Earth Space Defense (ESD), an international military defense and research organization, ably led by Director David Levinson. Through reverse engineering, the world has harnessed the power of alien technology and created an early warning system against future extraterrestrial invasions.
As the 20th anniversary of the invasion approaches, the threat of another attack looms large. An unidentified spherical ship emerges from a wormhole near Earth's Moon, and despite objections from scientists, is destroyed on the orders of the United Nations Security Council.
Defying orders, American pilots Jake Morrison and Charlie Miller then pick up Levinson, Marceaux, Umbutu, and U.S. federal controller Floyd Rosenberg on a space tug. They head for the wreckage in the Van de Graaff crater, where they recover a large container. An alien mothership suddenly appears, responding to the distress call, and proceeds to destroy much of the Earth's planetary defenses before landing over the North Atlantic Ocean, where it starts to drill down toward the Earth's molten core. Narrowly escaping death, those on board the space tug are able to avoid capture and return to Area 51.
Upon interrogation of one of the aliens held in captivity at Area 51's prison facility from the war, they learn that the aliens exist in eusociality and that one of their colossal Queens is commanding the invasion. Levinson hypothesizes that, if they kill the supervising Queen, her forces will cease drilling and retreat. A giant white sphere of virtual intelligence emerges from a rescued vessel and reveals that her mission is to evacuate survivors to a planet of refuge from worlds targeted by the aliens and has chosen the human race to assist in uniting all the oppressed worlds and lead the resistance in an attack on the Harvesters' planet.
Can the peace-loving worlds find a way to unite in an attack against the predators belonging to the Harvesters' planet? How will their mission to eliminate the Queen and destroy the Harvesters' planet unfold?