anuary 12, 2011 – A crew of astronauts led by Commander Jocinda “Jo” Fowler (Halle Berry) are doing maintenance at a satellite repair station. Jo’s friend, astronaut Brian Harper (Patrick Wilson), notices an unusual swarm of nanotech creatures heading toward them. The Swarm hits the satellite. Brian attempts to save his friend, Alan Marcus (Frank Fiola), but Brian gets knocked back by the Swarm, and Marcus is lost, along with another astronaut. Brian makes it to Jo’s shuttle and manages to fly themselves back to Earth.
18 months later, Brian has become disgraced by NASA after his reports of the Swarm attacking them are written off as crazy talk. His friendship with Jo suffers a fallout, and he ends up divorcing his wife Brenda (Carolina Bartczak). She moves to Jersey with their son Sonny, and he becomes distant from his father.
Ten years later, megastructurist KC Houseman (John Bradley) sneaks into the University of California to gather information on unusual moon activity. He goes to his regular job at a fast-food restaurant, where he gets confirmation of strange readings coming from the moon’s orbital trajectory. KC later goes to visit his mother Elaine (Kathleen Fee), who suffers from Alzheimer’s.
Jo still works at NASA but is now divorced from her ex-husband, General Douglas Davidson (Eme Ikwuakor). They share custody of their son Jimmy (Zayn Maloney), and Jo also houses foreign exchange student Michelle (Kelly Yu), who also takes care of Jimmy. At work, Jo is told of strange activity coming from the moon.
KC pretends to be Brian, as he was called to speak for a class field trip at a museum. When Brian actually shows up, KC attempts to present his readings and information about the moon getting closer to Earth, but Brian dismisses him and has security take KC out, but not before KC throws his info at Brian to read.
Brian now lives alone while Brenda has remarried Tom Lopez (Michael Pena) and has two daughters with him, Nikki (Ava Weiss) and Lauren (Hazel Nugent). Brenda calls Brian because Sonny (Charlie Plummer) is seen on the news being chased by the police. After he is arrested, Brian attempts to go to his bail hearing, but because of his interruptions and the lawyer saying “money is no object”, the judge postpones the hearing for a week, forcing Sonny to be in jail for that long. As Brian tries to bribe the judge into letting Sonny out, reports start to go out about the moon going out of orbit.
Jo’s colleagues estimate that they have about less than three weeks before the moon starts to break apart and send city-sized pieces of debris hurtling across the globe. NASA organizes a shuttle launch with a crew of three astronauts to go up to the moon and investigate the occurrence. The astronauts encounter the Swarm, and it surrounds the shuttle before breaking in and killing the astronauts, which is seen back at NASA. Panic around the planet begins to ensue, with looting and rioting going around. Soon, a tsunami hits California, wherein Brian has to help KC when he gets swept up by the water.
After Jo observes the footage from the shuttle and finds a hole dug into a crater floor, she digs into the old NASA archives and finds helmet cam footage from Brian’s suit during the first failed mission. She is found by a man named Holdenfield (Donald Sutherland), who works in the archives and implies that there is something about the 1969 moon landing that NASA is covering up.
Jo attempts to gather a crew for a second mission and is brought in to meet KC and Brian, the latter still being angry with her after he believes she threw him under the bus after their last mission. They learn about an EMP that was built to kill the Swarm, and they get a shuttle out of a museum to try and launch it into space. Before the mission is set, Brian arranges for Sonny to be released from prison to join Brenda and her family at Tom’s cabin in Colorado. He is joined by Michelle and Jimmy as they make the drive out there.
As another disaster is imminent, Jo and Brian act quickly to set the mission into motion, with KC being invited to join since he knows about mega structures more than they do. They all board the shuttle, just as a gravitational abnormality causes a huge ocean wave to come toward the city. The crew launches just before the water can hit them.
Sonny bonds with Michelle and Jimmy on the drive to Colorado, with Sonny speaking to Doug to assure him that Jimmy is safe. On their way, they are robbed by a trio of thieves, and they are forced to walk. Another gravitational shift causes people to be pulled up into the air, but Michelle holds onto Jimmy. They eventually make it to Tom’s place, but not before a crazy lady with a gun fires at them, thinking they are intruders.
In space, the trio make it to the moon and find the Swarm surrounding it. They place the bomb where the Swarm can grab it, but they notice that it stops short of touching the bomb. The Swarm proceeds to attack their shuttle until they disable their electronics. The crew determines that the Swarm is deliberately avoiding electronics. Jo believes that there are two separate entities on the moon, and one of them is trying to help them.
The trio make it onto the moon’s base, where Brian is met by the moon’s Operating System, which takes the form of Sonny as a child speaking to him. The OS explains that the Swarm is an artificial intelligence created by ancient humans. The Swarm took on a mind of its own and killed its creators before forming a base on the moon, feeding off the energy of a white dwarf in the core. The moon shifted out of orbit because the internal structure has destabilized. The OS tells Brian that the AI can be defeated, but a human must stay behind to make it happen.
Back on Earth, Sonny, Michelle, and Jimmy join Tom and his family as they have to evacuate. The thieves from earlier try to rob them, but Sonny and Tom hold them off with guns. As they try driving away, the thieves pursue them and attempt to run them off the road. The moon then causes another gravitational shift, where chunks of earth mass begin breaking off the ground. The leader of the thieves is crushed by debris, while the remaining two thieves crash their car against a chunk of mass after Sonny manages to drive off a ramp to safety. Meanwhile, the President of the United States issues an order for nukes to be launched at the moon in a last-ditch effort to save everyone.
Sonny, Tom, and everyone else put on oxygen masks as the air starts to thin, and they make their way to a cave for safety. Nikki’s oxygen runs low, so Tom gives her his tank. He starts to lose his breath and tells Nikki to just keep walking before he dies. When Nikki reaches her family, the oxygen starts to come back, so Sonny and Michelle attempt to go find Tom, but Sonny is taken down by a falling tree that pins him down.
The trio on the moon make one last attempt to get the bomb to the Swarm. Doug holds his colleagues at gunpoint to prevent them from nuking the moon since he believes Jo can still save them. When the trio gets close to the bomb, Brian attempts to sacrifice himself to stay behind and deliver the bomb, but KC ends up taking his place instead. He feels that Brian and Jo have families to return to, while he has a chance to have finally done something with his life. Brian and Jo bid him farewell, and the Swarm surrounds KC’s pod before he detonates the bomb, killing the Swarm and sending the moon back to its rightful position. Brian and Jo are close enough to the Earth to fly out on a pod.
Brian and Jo make it to be reunited with their families. Brian is told about Tom’s fate, and he tells Brenda that he was a great man. He also tells Sonny that KC saved the world.
Back on the moon, KC’s consciousness is uploaded to the base. He meets the Operating System, which takes the form of his mother. KC is told that they are about to get started on something big.