It was released by 20th Century Fox in 2D, 3D and IMAX 3D on June 24, 2016. The film was not well-received by critics, who found the plot and action sequences to be overblown and convoluted, though some praised its overall humor and playful delivery.
Twenty years after the events of the previous film, the international community recovers and the United Nations creates the Earth Space Defense (ESD), a united global defense program that serves as Earth's early warning system. The main defense force uses technology salvaged from the remains of the alien forces, with military forces assembled on the Moon, Mars, and Rhea, while the Area 51 base has become the Space Defense Headquarters.
In Africa, ESD Director David Levinson meets with Dr. Catherine Marceaux and warlord Dikembe Umbutu, who lead him to a completely intact alien destroyer that had concealed itself before being shut down after its mothership was destroyed. Umbutu's family had fought against the ship's alien crew and confiscated many of their weapons, which they now use. Aboard the ship, they discover that the ship was drilling a hole before the aliens' final defeat and had sent a distress call to its home planet. Furthermore, Umbutu and former U.S. President Thomas Whitmore experienced recurring visions of alien symbols ever since their personal encounters with the aliens.
A spherical ship teleports near the ESD's Moon defense headquarters. Levinson is convinced that it belongs to a different extraterrestrial race that is benevolent and urges the world's government not to attack; they order the ESD to shoot it down regardless. Against ESD orders, pilot Jake Morrison picks up Levinson, Marceaux, Umbutu, and Floyd Rosenberg on a space tug and they head for the crash site, where they recover a container. Suddenly, an alien mothership nearly ten times larger than the previous one appears and destroys the Moon base before approaching Earth. The space tug is caught in the mothership's gravitational pull, which lifts buildings and structures from most of Asia before being released over London. It manages to escape before heading to Area 51.
The mothership lands over the entire northern half of the Atlantic Ocean, destroying several cities in the process. It begins drilling a hole in the middle of the ocean to harvest the heat of Earth's core; this would destroy the planet in the process. The aliens also raid the Cheyenne bunker in Colorado and kill President Elizabeth Lanford along with most of her Cabinet. General Joshua Adams, a Cabinet official, is named the designated survivor and immediately sworn in as the 46th President.
Upon the space tug's arrival at Area 51, Dr. Brakish Okun wakes up from his twenty-year coma and opens the container, releasing a giant white sphere that reveals to the ESD that it was sent to help evacuate as many humans as possible to another planet to train them against the aliens, but cannot because the ESD destroyed the first ship, which was capable of evacuating humanity to the refuge planet. Meanwhile, Whitmore communicates with one of the aliens held in captivity since the last war. The ESD learns that the aliens, while similar to Earth's insect kingdom, are not like locusts as they initially believed and exist in eusociality, and that their queen is coming. ESD forces led by Captain Dylan Dubrow-Hiller stage a counterattack, but are caught in a trap within the mothership that disables their weapons. Dylan, along with Jake and fellow pilots Charlie Ritter and Rain Lao, manages to escape.
Seeing that its activity has alerted the alien queen to its presence, the sphere tries to convince the ESD to destroy it in order to prevent the aliens from getting the coordinates to the refuge planet. The remaining ESD forces instead use the space tug as a decoy and put the sphere in an isolation chamber, intending to lure the alien queen's ship to a secluded area and destroy it with nuclear weapons. Against his daughter Patricia's wishes, Whitmore volunteers to pilot the space tug on the suicide mission. During the subsequent battle, Whitmore leads the alien queen's warship to the trap and detonates the bombs, sacrificing himself and destroying the ship.
The alien queen survives using energy shields on her exoskeleton. Patricia personally flies a combat jet and destroys the queen's shields' projector, allowing Dylan, Jake, Charlie, and Rain to kill the queen before she can destroy the sphere, and the rest of the aliens flee. With the queen dead, the mothership stops drilling and retreats from Earth. Okun reveals that the sphere has asked them to lead a resistance against the aliens and offered them new technology in preparation for an assault on the aliens' home world.