Independence Day: Resurgence (2016) Plot Summary Explained

In the twenty years after the War of 1996, the United Nations has founded the Earth Space Defense (ESD), a global defense program using reverse-engineered alien technology and serves as Earth's defense force against extraterrestrial threats. Civilization has been restored, and relative peace among nations exists following the human race's victory over the aliens' attacks. The ESD set up bases from Area 51 to the Moon, Mars, and Rhea, and orbital defense satellites above Earth, as fortifications against future invasions.

ESD Director David Levinson meets with warlord Dikembe Umbutu and Dr. Catherine Marceaux in the African state République Nationale d'Umbutu. They travel to a landed alien saucer and discover that the aliens were drilling before sending a distress signal to their homeworld before their defeat. It is revealed that people such as former U.S. President Thomas Whitmore, Dr. Brackish Okun, and Umbutu are telepathically linked to the aliens' collective consciousness, following personal encounters, and have visions of an unidentified spherical object.

An unidentified spherical ship emerges from a wormhole near Earth's Moon. Despite objections from Levinson, the United Nations Security Council orders the ship to be destroyed. Defying orders, American pilots Jake Morrison and Charlie Miller then collect 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 holding a sphere. An alien mothership, over 3,000 miles in diameter, suddenly appears after responding to the distress call, and proceeds to destroy much of Earth's planetary defense systems before landing over the North Atlantic Ocean where it starts to drill down toward Earth's core for fuel that will destroy the planet in the process. Narrowly escaping death, the space tug avoids capture and returns to Area 51.

Whitmore, Levinson, and U.S. General Joshua Adams's groups interrogate one of the aliens held in captivity at Area 51's prison facility from the war. They learn that the aliens exist in a hivemind and that one of their colossal Queens is commanding the invasion. Realizing that they had killed a supervising Queen above Earth during the first invasion, Levinson hypothesizes that if they kill this one, her forces will cease drilling and go dormant. An ESD aerial fleet led by Captain Dylan Hiller stages a counterattack, but they are ambushed within the mothership, leaving only a few survivors, including Dylan, Jake, Charlie, and fellow ESD lieutenant and Chinese pilot Rain Lao.

In Area 51, Okun opens the rescued container and releases a giant white sphere containing a virtual intelligence. The sphere reveals that her mission is to evacuate survivors to a planet of refugees from other worlds targeted by the aliens, whom she calls "Harvesters", and unite them in an attack on the Harvesters' planet. In the mothership, all surviving ESD pilots manage to escape by hijacking enemy craft; Dylan, Jake, Charlie, and Rain navigate two Harvester fighters to pursue the Queen's personal ship, which is heading to Area 51 to extract information from the sphere about the refugee planet.

Knowing that the Harvester Queen has become aware of the sphere's location, the ESD hides her in an isolation chamber and uses a decoy in Jake's space tug to lure the Harvester Queen's ship into a trap. Whitmore volunteers to pilot the transport ship on a suicide mission, leading the Queen's ship into the trap before detonating a bomb, thus destroying the enemy ship by sacrificing himself. However, the Harvester Queen survives by using an energy shield of her own and another battle ensues, leading to the Harvester Queen finally being killed. Then all the remaining alien fighters are rendered inactive while the mothership stops drilling and retreats to space.

Okun reveals that the sphere has asked humanity to lead her resistance in preparation for an attack on the Harvesters' homeworld.