While working with a team from the University of Chicago on a project to convert hydrogen from water into clean energy, student machinist Eddie Kasalivich inadvertently discovers a sound frequency in his home laboratory that perfectly stabilizes their process the next day. As the team celebrates with a party at the project laboratory, Dr. Paul Shannon, the leader of the project, and Dr. Alistair Barkley, the project manager, debate whether or not to share the scientific discovery. Later that night, project physicist Dr. Lily Sinclair finds her car unable to start, so Eddie gets her home by bus. Back in the laboratory, Alistair and assistant Dr. Lu Chen prepare to upload their discovery to the Internet to share the breakthrough with the world, while a van approaches the premises. Chen hears a noise and goes outside to investigate, but is kidnapped by unknown assailants as Alistair is also attacked. Once he has dropped Lily off at Alistair's house, where she lives on the third floor, Eddie returns to the laboratory to retrieve his motorcycle but notices a suspicious van departing. Hearing alarms, he runs inside to find Alistair dead with a plastic bag over his head and Chen missing. As the hydrogen reactor has become dangerously unstable, Eddie, unable to deactivate it, speeds away as a concealed detonator triggers a massive hydrogen explosion that destroys the laboratory and eight blocks' worth of surrounding streets. Upon returning from questioning by the FBI, Eddie and Lily realize that they are being framed after encountering planted evidence in both of their houses. The two flee to an observatory in Wisconsin belonging to Maggie McDermott, an old friend of Eddie's. After resting up, they contact Paul but are almost caught and narrowly escape. As the pair are evading more police, Paul meets with Lyman Earl Collier at the C-Systems Research complex, where it is revealed that C-Systems orchestrated the plot to destroy the laboratory and frame the pair for it, with Lyman ordering the attack. Despite some disagreement, Paul and Lyman decide to continue hunting for the pair, a task facilitated when Eddie covertly arranges a meeting with Paul. At their rendezvous, Paul reveals his involvement in framing Eddie, but the meeting ends in an ambush in which Lyman's thugs Yusef Reed and Clancy Butler, who murdered Alistair, capture Lily while Eddie barely escapes. After tracing the license plate on the thugs' van, Eddie tracks them to the secret C-Systems Research facility where Paul and Lyman are forcing Lily and Chen to replicate the project. When C-Systems' test reactor malfunctions, Paul, the scientists and the prisoners all depart, allowing Eddie to furtively "fix" the system that night. The next morning, one of the other scientists discovers the working reactor and everyone celebrates. A suspicious Paul immediately obtains a download of the fusion data, and secretly gives it to his assistant, Anita, for safekeeping. He then encounters Eddie at a computer in the company boardroom, who demands his release for making the reactor work. Paul agrees but Lyman refuses, so Eddie sets the reactor to explode while sending proof of his innocence to the FBI and blueprints of the reactor to "hopefully a couple thousand" international scientists. Lyman responds by shooting Chen dead, then locking in Eddie and Lily to die in the explosion as he, Paul, and their staff flee the site. Lyman is given a falsified copy of the fusion data before Paul kills him for overstepping the bounds of the program, leaving his body in an elevator. During his own escape, he deactivates the containment system, allowing Eddie and Lily to escape. They are attacked by Reed and Butler over an ascending construction lift but escape by climbing aboard it moments before a blast wave sweeps through the complex, incinerating the corpses of Reed, Butler, and Lyman. Having survived the shockwave, Eddie and Lily are met by FBI agents Ford and Doyle, now convinced of their innocence, who take them to safety. Paul is shown dictating a memo to Anita in a chauffeured limo, informing the Director of the CIA that "...C-System no longer a viable entity." In a post-credits scene, the C-Systems facility is seen imploding into the landscape.

Ten years after defeating Hades' Kraken, Perseus, the demigod son of Zeus, now lives as a fisherman with his son Heleus, after the death of his wife Io. Zeus visits Perseus, warning him that, since humans stopped praying to them, the gods are losing their powers and becoming mortal. They can no longer sustain the walls of Tartarus which are holding back the imprisoned Titan Kronos with him. Perseus, valuing his family's safety, refuses to help. Zeus meets his brothers Hades and Poseidon and his son Ares in Tartarus. He asks Hades for help in rebuilding Tartarus' walls, but Hades rejects the offer and attacks Zeus, as does Ares. Poseidon is fatally injured in the ensuing fight. Hades and Ares imprison Zeus, stealing his thunderbolt. They plan to make a deal with Kronos: in exchange for remaining immortal, they will drain Zeus' divine power to revive Kronos. The walls of Tartarus break, unleashing monsters onto the world. After killing a two-headed Chimera in his village, Perseus decides to see Zeus. He instead finds a dying Poseidon who informs him of the situation and tells him to find his demigod son Agenor, who will lead him to Hephaestus, who knows the way into Tartarus. Poseidon then gives Perseus his trident and succumbs to his injuries. Perseus, Andromeda and Agenor set out to find Hephaestus on a hidden island. Agenor explains that Hephaestus created three weapons which Zeus, Hades, and Poseidon wield: Zeus' thunderbolt, Hades' pitchfork, and Poseidon's trident, which can jointly form the Spear of Trium, the only weapon that can defeat Kronos. After an encounter with three Cyclopes, the travelers eventually meet the now-mortal Hephaestus and reach the entrance of a labyrinth leading to Tartarus. Hephaestus sacrifices himself during an attack by Ares to enable Perseus, Andromeda, and Agenor to enter the labyrinth. Inside the labyrinth, a Minotaur attacks Perseus, who kills it. The group eventually enters Tartarus. Meanwhile, Zeus has been almost entirely drained of power as Kronos awakens. Zeus apologizes to Hades for banishing him to the underworld and asks his forgiveness, as he has forgiven Hades for his actions. Hades decides to help Zeus and stop Kronos in contrast to Ares. Perseus arrives and frees Zeus. Ares wounds Zeus with Hades' pitchfork, allowing Perseus to obtain it before he and the others escape Tartarus with Zeus. Aiming to retrieve Zeus' thunderbolt from Ares in order to defeat Kronos, Perseus challenges him to a duel. Meanwhile, Andromeda's army is overwhelmed by the Makhai. Hades revives Zeus and together they defeat the creatures. Kronos appears and begins to attack Andromeda's army. Zeus and Hades hold off Kronos while Perseus duels Ares, eventually killing him with the thunderbolt. Combining the gods' weapons into the Spear of Trium, Perseus destroys Kronos by traveling to his heart and throwing the spear into it. Zeus reconciles with Perseus and then dies of his wounds and Hades leaves, accepting mortality. Heleus tells his father that he wants to return to his life as a fisherman, but Perseus tells him they cannot, and encourages Heleus to be proud of himself, as he is the son of Perseus and the grandson of Zeus, with Perseus giving his sword to Heleus.

Foster brothers John and Charlie Robinson are decoy transit cops patrolling the New York City Subway. Chasing muggers into a subway tunnel, John and Charlie are furious when one of the teenage thieves is gunned down by officers guarding the money train, hauling subway revenue. A brawl ensues, and transit captain Donald Patterson blames the brothers for delaying the money train. Charlie owes $15,000 in gambling debts to mobster Mr. Brown, who nearly has him thrown off a building before John intervenes, promising to pay the money his brother owes. John and Charlie both take a liking to Grace Santiago, a newly assigned decoy officer. When a serial arsonist known as Torch sets a token booth on fire, the decoy squad rescues the booth attendant, but Torch escapes after a struggle with Grace. The squad is temporarily assigned to the money train, where another brawl earns Grace and the brothers Patterson’s displeasure. John rejects Charlie's plan to rob the train on New Year's Eve, with less security and up to $4 million on board. He gives Charlie the money to settle his debt, but Charlie is pickpocketed by an old lady on the train. Grace and John give in to their mutual attraction, while Charlie is badly beaten by Brown’s men, and is saddened to spot Grace and John sleeping together. Grace poses as a token booth attendant in a sting operation to apprehend Torch, who recognizes her and realizes the trap. Distracting the police by pushing a man in front of a train, Torch sprays Grace with gasoline but Charlie alerts the other officers, who open fire. Chasing Torch to the street, Charlie saves two children from a runaway carriage. John pursues the killer to another station, where Torch is burned by his own gasoline and killed by an oncoming train. Patterson fires Charlie and John over the failed operation, leading to a falling out between the brothers. Mr. Brown warns Charlie that he will have John killed if his debt is not paid by New Year's Day, and a desperate Charlie prepares to rob the money train. John storms into Brown's strip club and fights off the mobsters, threatening Brown not to harm his brother. On New Year’s Eve, Charlie sneaks aboard the money train through a floor panel, throwing out the driver and reaching a maintenance ladder to Central Park, but is unable to escape due to mounted cops nearby. Realizing Charlie’s plan, Grace convinces John to intervene. John reaches the train and helps Charlie avoid arrest, disabling the brakes and smashing through a steel barricade. Patterson recklessly diverts the train onto a track occupied by another train, willing to put the passengers in danger to secure the money train. The runaway money train rams into the passenger train, threatening to derail both trains. With no brakes and the throttle jammed, the brothers throw the money train into reverse to save the other train, leaping onto the roof of the passenger train as the money train derails. Slipping into the crowd at the station, the brothers come face to face with Patterson, who spits in John’s face. Fed up with his abuse, they both punch Patterson, who is arrested by Grace for endangering the passengers' lives. The brothers emerge in Times Square as the new year begins, but their celebration turns to bickering as John realizes Charlie has kept over $500,000 from the money train.

In 2034, computer programmer Ken Castle invents self-replicating nanites that replace brain tissue and allow humans to control other humans' actions and see through their eyes. The first application of Castle's "Nanex" technology is a virtual community life simulation game, Society, which allows gamers to manipulate live actors as their avatars. Society becomes a worldwide sensation, making Castle the richest man in the world. He then creates Slayers, a third-person shooter where the "characters" are death-row prisoners using real weapons in specially designated areas. Unlike Society actors, Slayers participants are not paid; instead, they volunteer, and any Slayer who survives 30 matches will earn their freedom. John "Kable" Tillman is everyone's favorite, having survived a record 27 matches, and is controlled by 17-year-old gamer Simon Silverton. An activist organization called the "Humanz" hacks a talk-show interview with Castle and claims that his technology will one day be used to control people against their will. The Humanz also disrupts Society play, but Castle sees both these actions as trivial. However, Castle feels threatened by Kable's winning streak and introduces a new inmate into Slayers, Hackman, specifically to kill Kable. Unknown to anyone else, Hackman will not be controlled by a player, thus not be handicapped by the "ping" that causes a small but dangerous delay between the player's command and the Slayer's action. Kable's estranged wife, Angie, works as a Society character, but in spite of her earnings, she is refused custody of their daughter, Delia, who has been placed with a wealthy foster family. The Humanz contact Kable and Simon separately and offer to create a mod that will let him escape, but only if Simon relinquishes control during the game. Simon is even given a mod to speak freely to Kable. The escape is successful, and news outlets report that Kable has been fragged, which puts Simon in a difficult position: he is labeled a "cheater", locked out of his account which is spammed with hate mail, his father's asset frozen, and arrested by the FBI for helping Kable escape. Kable is brought to the Humanz' hideout; he refuses to help their fight against Castle but learns of Angie's current location in Society. He rescues her, escaping from both Hackman and Castle's security forces. Gina, the talk show host who secretly assists the Humanz, meets them. The Humanz deactivates the nanites in Angie and Kable's brains, and Kable remembers that the original nanites were tested on him while he was still in the military. Under Castle's control, Kable shot and killed his best friend and was imprisoned. Upon learning that Castle is the wealthy father who adopted Delia, Kable infiltrates his mansion to get her back. He locates Castle, who reveals that his henchmen have already tracked down the Humanz' lair and killed all of them. He also reveals that 98% of his own brain has been replaced with nanites, but this allows him to control others rather than be controlled. He plans to release airborne nanites, which will infect the entire country within six months, giving him ultimate control. Hackman attacks Kable, who easily kills him. Kable then attacks Castle but is frozen in place as Castle explains that his men have reactivated his and Angie's nanites. Unknown to Castle, Gina and Trace escape and patch into the Nanex, exposing the confrontation to the world and exposing Castle's plans worldwide. They also restore Simon's account, restoring access of Kable. Castle tries to manipulate Kable into killing his own daughter, but he resists, allowing Simon to control him and attack Castle. He and Simon wrestle for control, but Kable tells Castle to imagine his knife stabbing him. Castle unconsciously does so, allowing Kable to kill him and removing his control over everyone. With Castle dead, Kable convinces his technicians to deactivate the Nanex, freeing all the "characters" in Society and Slayers.

Due to the 21-century ecological crisis on Earth, for twenty years humankind has been terraforming Mars as its new home by sending algae to its surface. When oxygen levels begin decreasing, Mars-1 is sent to investigate, under Mission Commander Kate Bowman with a crew consisting of egotistical co-pilot Ted Santen, science officer Bud Chantilas, mechanical systems engineer Robby Gallagher, and two civilians: bioengineer Quinn Burchenal, and terraforming expert Chip Pettengill. Rule-breaking Gallagher is not Bowman's first choice, and while the crew nicknames him "space janitor," the two are drawn to each other. A gamma-ray burst resulting from a massive solar flare damages the ship as it reaches Mars. Bowman launches the crew to the planet's surface, and manages to eject the flames of a ship-wide fire into the vacuum and restore power to communicate with Houston. She learns that Mars-1's orbit will decay in 31 hours, but that they can burn to return to Earth before that occurs. The landing craft tumbles to the wrong location, and AMEE, the military robot navigator, is jettisoned. Chantilas is mortally wounded and tells the others to leave without him to save oxygen. The landing party finds no algae on the planet's surface, then discover that the HAB 1 has been destroyed, ensuring death when their spacesuit oxygen runs out. Pettengill follows Santen to the edge of a cliff, but when Santen mocks him, Pettingill strikes him, and he falls over the edge. Petengill then tells the others that Santen committed suicide. Gallagher decides to die quickly and opens his helmet, only to discover that Mars's atmosphere contains oxygen, more than the failed terraforming would have produced. Burchenal realizes they are near the Pathfinder rover, which will possibly have a working radio to contact Bowman. The trio set fire to the ruins of HAB 1 to warm them during the night. AMEE rejoins the crew, but when they discuss shutting it down and taking its guidance device, it switches to a military protection mode, wounds Burchenal and leaves, intent on picking off the crew one at a time. When they reach the Rover, Gallagher is able to build a radio; Houston picks up their signal on a long-unused frequency and alerts Bowman. Bowman tells them to hike to Kosmos, a failed Russian probe 100 km away, and launch themselves by fitting into the rock sample container, but later tells Gallagher the space will hold only two passengers. As they shelter in a cave from an ice storm, Gallagher tells the other two they'll be launching on Kosmos. Pettengill doesn't believe Gallagher will sacrifice himself. Meanwhile, Bowman receives orders from Houston that since it is unlikely the crew survived the ice storm, she is ordered to return home. Burchenal and Gallagher awaken to discover Pettengill has fled with the radio, then watch as he is chased and killed by AMEE. They recover the radio and find Pettengill's body in a patch of algae, full of Martian nematodes. Burchenal deduces that the nematodes have been eating the algae and excreting oxygen, and he captures a few in a sample vial as they could possibly save Earth. Drawn to Burchenal's wounds, the nematodes swarm him and start chewing through his suit. He tosses the vial to Gallagher and immolates himself. The burst, which consumes the algae patch and nematodes, is seen from Bowman on the Mars-1. She is able to contact an exhausted Gallagher and urges him to get to Kosmos. Gallagher discovers the Russian probe's battery is dead, and right before the Mars-1 enters communication blackout he tells Bowman to leave. Gallagher then bids her goodbye when AMEE flies overhead and he realizes he could use AMEE's core as a power source. He lures and disables AMEE with one of the probe's sample launchers, removing AMEE's battery before it self-destructs, then launches himself into orbit. Bowman sees the Kosmos in the path of the Mars-1, aborts her departure and tethers out to retrieve and then revive Gallagher, who is in cardiac arrest. Later, as Bowman tells him that Earth now considers him a hero, she admits he's not who she thought he was, and they finally kiss. The film ends with her voiceover musing that on the six-month journey home, she'll get to know the janitor.

On August 12, 2011, hostile alien spacecraft make landings off the coasts of large cities. Los Angeles is evacuated while Marines from Camp Pendleton arrive, including Staff Sergeant Michael Nantz, an Iraq War veteran. Nantz, who was to begin his retirement, is assigned to the 1st Platoon, Echo Company, of the 2nd Battalion, 5th Marines. Under the command of 2nd Lieutenant William Martinez, the platoon arrives at a forward operating base (FOB) established at Santa Monica Airport. The alien ground forces have no apparent air support while using rapid dominance. Hence, the Air Force prepares a carpet bombing of the Santa Monica area, and the platoon is given 3 hours to retrieve civilians from a police station. As they advance through Los Angeles, they are ambushed and suffer multiple casualties. Nantz takes Marines Imlay and Harris to look for Lenihan, who is missing from the group. After fighting off an alien, they team up with some soldiers from the Army's 40th Infantry Division and an Air Force intelligence technical sergeant, Elena Santos. At the police station, the makeshift platoon finds five civilians: veterinarian Michele, children Kirsten, Amy, Hector, and Hector's father Joe. A helicopter arrives to evacuate wounded Marines but cannot take on the weight of the civilians. During takeoff, it is destroyed by alien air units, killing Grayston, Guerrero, Lenihan, and Simmons. The Marines commandeer an abandoned transit bus for the evacuation. En route, they deduce that the alien air units are drones that target human radio transmissions; Santos reveals that her mission is to locate and destroy the aliens' command center controlling the drones. When their bus comes under attack by aliens on an elevated freeway, the Marines rappel the group to street level. In the ensuing battle, Marines Stavrou and Mottola and the remainder of the California Army National Guard soldiers are killed, while both Joe and Lieutenant Martinez are wounded. Martinez uses his radio to attract the aliens, then detonates explosives, sacrificing himself for his team. Nantz is now in command of surviving personnel Santos, Imlay, Kerns, Lockett, Harris, Adukwu, and the civilians, continuing their escape from the bombing zone. A scientist speculates on news media that the aliens seek Earth's water resources for fuel while exterminating the human population. The planned carpet bombing fails to materialize. Reaching the FOB, the Marines find it destroyed, and the military retreats from the city. The Marines plan to escort the civilians to an alternate extraction point. When Joe dies from his wounds, Nantz comforts Hector. Lockett confronts Nantz regarding his brother, a Marine who, with four others, was killed during Nantz's last tour. They come to peace when Nantz explains that he continues to think of them and recites each one's name, rank, and serial number. Nantz motivates the group to move forward to honor their fallen comrades, including Joe, for his bravery. They reach the extraction point and evacuate by helicopter. In flight, the chopper experiences a brief loss of power. Nantz theorizes that they are flying near the alien command center, transmitting intense radio messages to its drones. He orders his unit to accompany the civilians while he stays to reconnoiter the area, but his marines join him. Searching through sewers, they confirm the presence of a large alien vessel. Kerns radios to request missiles, which Nantz manually directs using a laser designator while the others defend his position. Kerns is killed when a drone hones in on his radio, but the Marines succeed in guiding a missile to the command module, which is destroyed. The uncontrolled drones fall from the sky, and the alien ground forces retreat. The remaining marines—Nantz, Imlay, Lockett, Harris, Adukwu, and Santos—are evacuated to a base in the Mojave Desert, greeted as heroes. They are told that their successful plan has been transmitted to the militaries battling alien forces in other cities, that Michele and the three children were rescued, and that they can now rest. Instead, they re-arm and depart to retake Los Angeles.

The diminutive Agent 00, the number 1 agent from the Secret Agency, is provided with a number of new hi-tech gadgets from his boss, and then sent to stop the mysterious warlord Mr. Giant, who has just kidnapped Dr. Kohler, a foreign scientist visiting Manila to offer his latest invention, the N-Bomb, to the government. Mr. Giant intends to use the lethal weapon to take over the world, but Agent 00 is ready to stop him. He can count on the help of Irma, a fellow agent who has infiltrated Mr. Giant's criminal organization, working for the drug traffickers that are headed by a gangster named Cobra. This leads to many battles between Agent 00 and the villain's henchmen. Once Irma's cover is blown, she is taken prisoner as a bait and sent to Mr. Kaiser, Mr. Giant's second-in-command, who keeps her in his lair. In order to find Kaiser, Agent 00 enlists the help of other Bond girl types, such as night club enthusiast Anna and criminal reporter Marilyn, romancing his way to their allegiance. After flushing out and killing criminal bosses of increasing importance, and all of their henchmen, Agent 00 reaches Kaiser, but by then Irma has been shipped to Hidden Island, Mr. Giant's super-secret lair. After finding the secret location of the island, Agent 00 uses a prototype size-compatible jet pack to get there, and calls for reinforcements. He confronts and kills Mr. Giant himself (who is revealed to be a dwarf himself, although taller than Agent 00), then along with the squad of agents from the Secret Agency, Agent 00 and Irma clean the island of all remaining henchmen. However, right after a freed Dr. Kohler has finally reached safety, Irma is shot and killed. In the final scene, Agent 00 is seen paying respect on her tomb.

In 1996 Brooklyn, Molly Wright witnesses her parents being neuralyzed by agents of Men in Black after they see an alien in their home. Molly helps the alien escape, avoiding neuralyzation herself. Twenty-three years later, rejected from government agencies due to her "delusions" regarding alien life, Molly tracks down an alien landing and follows MIB agents to their headquarters in New York City. Caught entering the agency, Molly makes an impression on Agent O after revealing she had bypassed neuralyzation, arguing that her obsessive search for them makes her "perfect" for the job and she has no life outside her search for the agency. She is awarded probationary agent status as "Agent M" and assigned to the organization's London branch. There, M meets High T, head of the London branch, and Agent H. M learns that H and T fought off an invasion of the Hive, a parasitic race who invade planets by merging with the DNA of the conquered species, at the Eiffel Tower in 2016, using a wormhole included in the original migration to Earth. H has since become unconcerned with his duties and only keeping his job due to High T covering for him. M arranges for herself to be assigned to assist H in his meeting with alien royalty Vungus the Ugly, H's close friend. During their night out with Vungus, they are accosted by mysterious alien Twins able to manifest as pure energy. The Twins fatally injure Vungus, who gives M a strange crystal before he dies, claiming that H has changed since they last met and cannot be trusted. M points out that few people knew Vungus' location, and he was likely betrayed by one of the agents present when High T assigned H to guard him. Nervous at the possibility of a traitor within MIB, High T assigns Agents C and M to investigate while H is demoted to desk duty, with evidence suggesting that the Twins had DNA traces of the Hive. H convinces M to join him in following a lead to Marrakesh, where they recover "Pawny", the last survivor of a small group of aliens attacked by the Twins. Pawny pledges loyalty to M, and they are trapped by MIB agents coordinated by C, who recovered video footage of Vungus passing the crystal to M and believes she is the traitor. With the aid of alien contacts Nasr and Bassam, H escapes with M and Pawny on a rocket-powered bike, and they learn that Vungus' crystal is a weapon powered by a compressed blue giant. As they repair the damaged bike, Bassam steals the weapon and takes it to H's ex-girlfriend Riza Stavros, an alien arms dealer. Traveling to Riza's island fortress, the trio attempts to infiltrate the base, but is caught by Riza and her bodyguard Luca Brasi. Luca, the alien M rescued as a child, returns the favor by allowing them to leave with the weapon while he keeps Riza contained. The three are cornered by the Twins, who are killed by High T and a group of agents. Although the case appears concluded, H and M review the evidence and realize that the Twins' phrases suggest they required the weapon to use against the Hive, especially when the only evidence of Hive DNA was provided by High T. They discover High T has deleted the case file and not sent the weapon to evidence, and has gone to the Eiffel Tower with the weapon. C also realizes High T's deception and allows H and M to follow High T to the Eiffel Tower. As they travel to the reopened wormhole, M's questioning of H's memory of the Hive's defeat reveals he was neuralyzed when the Hive converted T into one of their own during the battle. The High T/Hive hybrid activates a wormhole to draw the Hive to Earth, but H draws out High T's true personality long enough for M, with the help of Pawny, to use the weapon at full capacity to destroy both the hybrid and the Hive infestation trying to reach Earth. With the truth of T's conversion exposed, Agent O joins H and M in Paris, where she grants M full agent status and appoints H probationary head of MIB's London branch.

Gregorio and Ingrid Cortez are spies with two children, Carmen and Juni, whom they shield from their lives to protect them from inherent danger. They work for the Organization of Super Spies (OSS) doing office consultant work, but are suddenly called back to active field work to find missing agents. Gregorio suspects children's television host Fegan Floop has kidnapped them, mutating them into his "Fooglies" – creatures on his show, a program that Juni avidly watches. The children are left in the care of their uncle, Felix Gumm. Gregorio and Ingrid are captured by Floop's "Thumb-Thumbs" (robots whose arms, legs, and heads resemble oversized thumbs) and taken to his castle. Felix is alerted to the parents' capture, activates the fail-safe, and tells the children the truth about their parents, and that he is not their uncle, but an agent sent to watch over them. The house is attacked by Ninja Thumb-Thumbs, and Felix is captured while the children escape alone via a miniature submarine set to autopilot to a safe house. At the safe house, the children accept that their parents were spies and decide to rescue them. Inside Floop's castle, he introduces his latest creation, small child-shaped robots, to Mr. Lisp. They plan to replace the world leaders' children with these super-strong robots to control the world, but since the androids have no artificial intelligence yet, they are unable to function outside their regular programming. Lisp is furious, demanding usable androids. Floop, with his second-in-command Alexander Minion, interrogates Gregorio and Ingrid about 'The Third Brain'. Ingrid knows nothing of it, while Gregorio claims he had destroyed the brain years ago. After Floop leaves, Gregorio reveals to Ingrid that the Third Brain was a secret OSS project he had worked on: an AI brain with all the skills of the entire OSS. The project was scrapped for being too dangerous, and many scientists demolished the brains that they were working on, but Gregorio refused to destroy the final prototype. At the safe house, Carmen and Juni are visited by OSS agent Ms. Gradenko. Giving Carmen a bracelet as a sign of trust, she asks about the Third Brain, but Carmen is confused. Gradenko orders the house to be dismantled, and the siblings realize Gradenko is a traitor when they see ninja Thumb-Thumbs destroying the escape submarine. With Gradenko's intentions revealed, Juni accidentally exposes the Third Brain, and a chase ensues. Carmen gets the brain, and she and Juni escape. She realizes too late that the bracelet from Gradenko has a tracking device, and she and Juni are attacked by their robot counterparts, who steal the Third Brain and fly away. Meanwhile, back at the castle, Gregorio tells Ingrid that Minion used to work for the OSS, but was fired after he reported him tampering with the Third Brain project. With it, Floop can achieve his goal, but he wishes to continue his children's TV show. Minion has different plans and takes over, locking Floop inside his "virtual room", the chamber where he films his television series. Carmen and Juni receive reluctant help from Gregorio's estranged brother Isador "Machete" Cortez when they show up at his spy shop. He refuses to accompany them, so they steal some gear and take his spy jet to fly to Floop's castle. After a few mishaps, Carmen and Juni eject themselves from the plane before it crashes into the castle, and they enter via the underwater entrance. While the children infiltrate the castle, Juni rescues Floop, who helps him and Carmen release their parents. Together, they trap Minion in Floop's Fooglies machine, mutating him into a Fooglie. Confronting Lisp and Gradenko, the family is beset by all 500 robot children. Suddenly, Machete busts through the window, reconciling with Gregorio and joining the family to fight. However, at the last moment, Floop reprograms the robots to change sides. The 500 superhuman robots quickly overpower Minion, Lisp, and Gradenko. With advice from Juni, Floop introduces the robot versions of Carmen and Juni on his show. At home, some time later, the family's breakfast is interrupted by Devlin, the head of the OSS, with a mission for Carmen and Juni. The children tell him they will only accept if all the Cortezes can work on the mission together as a family.

When a mission to retrieve a stolen suitcase bomb goes awry, CIA agent Kevin Pope is killed. Pope was working undercover as an antiquities dealer under the name Michael Turner. The CIA, which is desperate to complete the mission, discovers that Agent Pope had a twin brother, Jake Hayes, from whom he was separated at birth; their mother died giving birth and Hayes suffered from a severe lung infection that prompted the doctors to separate them because they felt that Hayes was unlikely to live for very long. Hayes hustles chess games, scalps tickets, and works at small clubs in Jersey City, New Jersey, to make ends meet. Meanwhile, Hayes's girlfriend, Julie grows tired of waiting for him to grow up and decides to move to Seattle, Washington. After the CIA successfully persuades Hayes to participate and begins to train Hayes for a mission that is to take place in Prague, Czech Republic, they are initially dismayed by his lack of refinement. Agent Gaylord Oakes confronts Hayes, telling him he does not trust him. When Hayes begins paying attention, the CIA sets him up in his brother's old apartment in Manhattan to test him and try to bait the men who killed his brother. Hayes is attacked, but escapes unharmed. Looking for a way out, Hayes goes to his foster mother only to be found by Oakes, who persuades him to finish the mission. After arriving in Prague, Hayes – posing as his dead brother – meets with the men selling the suitcase bomb. The seller, Adrik Vas is an ex-Russian Army Colonel with ties to the Russian Mafia. When they return to their hotel, Hayes is greeted by his brother's ex-girlfriend Nicole. Believing Hayes is his brother, she dines with him and returns to his hotel, where the couple is ambushed by rival buyers. Nicole figures out that Hayes is not his brother and returns to her assignment covering the Balkans for CNN. Hayes and Oakes meet with Vas and are able to steal the arming codes. Just as they close the deal, Vas' men double cross them with the rival buyer. When the rival dealers, who are part of a multi-national terrorist organization, learn they cannot detonate the bomb because of the missing codes, they kidnap Julie. Hayes gives himself up trying to save his girlfriend, and the terrorists get the codes back and arm the bomb. After interrogating one of the captured terrorists, they track the bomb to Grand Central Station. With the clock ticking, they locate the bomb and the terrorist leader Dragan Ađanić, who has started the countdown. Oakes rescues Hayes by killing two terrorists. As Hayes starts to enter the codes to disarm the bomb, Ađanić holds Julie hostage. To distract Ađanić, Hayes pretends to shoot Oakes, and they kill Ađanić by shooting him repeatedly. Hayes is able to disarm the bomb just prior to detonation. Hayes visits his brother's grave. Later, Oakes approaches Hayes at his wedding to Julie and warns him that a dangerous criminal has escaped from prison and is seeking revenge on Kevin Pope, but since Kevin is dead and Hayes was impersonating him, the criminal thinks Hayes is Kevin. Hayes begins to panic and demands that Oakes protect him, but Oakes laughs as he reveals that it was only a joke and he really just came for the wedding.

Doug Masters, son of veteran USAF pilot Colonel Ted Masters, is a hotshot civilian pilot hoping to follow in his father's role. He receives a notice of rejection from the USAFA and Colonel Masters has been shot down and captured by the fictional Arab state of Bilya while patrolling over the Mediterranean Sea. Though the incident occurred in international waters, the Arab state's court finds Colonel Masters guilty of trespassing on its territory and sentences him to hang in three days. Deciding that the U.S. government will do nothing to save Colonel Masters' life, Doug devises his own rescue mission. He requests the help of Col. Charles "Chappy" Sinclair, a Vietnam veteran pilot currently in the Air Force Reserve, who, though he did not know Colonel Masters personally, had a favorable encounter with him years earlier and "knew the type." Chappy is initially skeptical but Doug convinces him that, with his friends, he has full access to the airbase's intelligence and resources and can give him an F-16 fighter for the mission. To Doug's surprise, Chappy had already begun planning a rescue operation after learning the outcome of Colonel Masters' trial. The team of Chappy and Doug devises a meticulously planned mission and procures two heavily armed F-16B jets, with Doug flying the second. On the day of Colonel Masters' scheduled execution, Doug and Chappy fly their jets to the Mediterranean Sea and cross into Bilyan airspace. The Bilyan military responds and in the ensuing battle, Doug and Chappy take out three fighters and destroy an airfield, with Chappy's plane being hit by anti-aircraft fire. He tells Doug to climb to a high altitude and play the tape he made the night before. Doug then listens as Chappy's engine fails and crashes into the Mediterranean Sea. Chappy's recorded voice gives Doug encouragement and details that help him to complete the mission and rescue Colonel Masters. Making the enemy believe he is leading a squadron, Doug threatens the enemy state into releasing Colonel Masters for pickup at an airfield. Before Doug lands his F-16, Colonel Masters is shot by a sniper, causing Doug to destroy the airbase and engulf the runway with napalm to keep the army at bay while he lands and picks up his wounded father. Just as they take off, Doug and Colonel Masters encounter another group of MiGs led by Col. Akir Nakesh, himself an ace pilot. The lone F-16 and Nakesh's MiG engage in a dogfight until a missile from Doug finishes off Nakesh. Low on fuel and ammunition, the F-16 is pursued by the other enemy MiGs when a flight of U.S. Air Force F-16s appears, warding off the MiGs before escorting Doug and Colonel Masters to Ramstein Air Base in West Germany. While Colonel Masters is being treated for his wounds, Doug is reunited with Chappy, who had ejected from his plane and was picked up by an Egyptian fishing trawler. The two are summoned by an Air Force judiciary panel for their reckless actions. Seeing that any punishment for the duo would expose an embarrassing lapse in Air Force security, the panel forgoes prosecution, provided that Doug and Chappy never speak of their operation to anyone. In addition, Chappy convinces the panel to grant Doug admission to the Air Force Academy. Days later, a plane assigned by the President returns to the U.S., reuniting Doug, Chappy and Colonel Masters with family and friends.

In 1982, Sam Brenner and his friends Will Cooper and Ludlow "The Wonder Kid" Lamonsoff play at an amusement arcade together before Brenner participates in a video game championship, where he seemingly loses a Donkey Kong match to Eddie "The Fireblaster" Plant. Videotaped footage of the event is put in a time capsule that gets launched into outer space. In the present, Brenner, now an electronics installer, is summoned alongside lieutenant colonel Violet van Patten to the White House, where Cooper, now President of the United States, shows surveillance footage of a besiegement at the Andersen Air Force Base in Guam. Brenner notes the attack's resemblance to the game Galaga, but Admiral James Porter of the United States Navy strongly advocates against its inference in the case. Brenner meets up with Lamonsoff, who reveals the attack was caused by an alien force that mistook the time capsule's footage as a declaration of war and are now challenging Earth to a best-of-three battle using technological recreations of the championship's games, claiming they have won the first match. Brenner and Lamonsoff inform Cooper of a coordinated aim at India, but he dismisses their concerns. After the aliens win the second match by demolishing the Taj Mahal as Arkanoid, Brenner and Lamonsoff train Navy SEALs to play the games while van Patten develops effective rayguns. Calling themselves the "Arcaders", the team heads to London, where the aliens attack Hyde Park as Centipede before being repelled by Brenner and Lamonsoff. Cooper, Lamonsoff and Brenner recruit a convicted Eddie to assist in New York City, where the Arcaders battle a giant Pac-Man in Mini Coopers representing the ghosts. After Brenner defeats Pac-Man, the Arcaders receive Q*bert as a trophy. During a celebration at the White House however, the aliens announce that one of the Arcaders has cheated, meaning Earth forfeits the challenge. Before being abducted by the aliens, van Patten's son Matty discovers Eddie cheated in the fight against Pac-Man using a code written on his glasses, which he also used in the 1982 video game championship. The aliens attack Washington, D.C. with an army of 1980s video game characters. With Cooper and a repentant Eddie's help, the Arcaders fight through the onslaught while Lamonsoff persuades Lady Lisa, a video game character whom he has a crush on, to join them. Brenner, Violet, Will and Q*bert are summoned to the aliens' mother ship for a final chance to save Earth by facing the aliens' leader as Donkey Kong. The group is placed on the game's starting level, with Donkey Kong and the captives at the top level. Struggling against the obstacles, Brenner loses hope until Matty reveals Eddie's cheating. Realizing he actually is the world's best Donkey Kong player, Brenner regains his spirit and defeats Donkey Kong, resulting in the aliens' forces, including Lisa, being neutralized. The Arcaders are hailed as heroes as Will negotiates a peace agreement with the aliens. Eddie apologizes to Brenner for cheating and acknowledges him as the best Donkey Kong player. Seeing Ludlow devastated over Lisa's termination, Q*bert cheers him up by shapeshifting into her. Brenner and van Patten begin a relationship, Eddie meets Serena Williams and Martha Stewart as he requested and the aliens return to their home planet.