The Asgardian Loki encounters the Other, the leader of an extraterrestrial race known as the Chitauri. In exchange for retrieving the Tesseract, a powerful energy source of unknown potential, the Other promises Loki an army with which he can subjugate Earth. Nick Fury, director of the espionage agency S.H.I.E.L.D., and his lieutenant Agent Maria Hill arrive at a remote research facility during an evacuation, where physicist Dr. Erik Selvig is leading a research team experimenting on the Tesseract. Agent Phil Coulson explains that the object has begun radiating an unusual form of energy. The Tesseract suddenly activates and opens a wormhole, allowing Loki to reach Earth. Loki takes the Tesseract and uses his scepter to enslave Selvig and a couple of agents, including Clint Barton, to aid him in his getaway.
In 1961, the Ark, a Cybertronian spacecraft carrying an invention capable of ending the war between the Autobots and Decepticons, lands on the far side of the Earth's Moon. The crash is detected on Earth by NASA, and President John F. Kennedy authorizes a mission to put a man on the Moon as a cover for investigating the craft. In 1969, the crew of Apollo 11 lands on the Moon to explore the craft.
Sixty-five million years ago, the alien race known as the "Creators" invade Earth, wiping out most of life on the planet including the dinosaurs with the "Seeds", and cyber-form thousands of planets, including Cybertron. In the present, Darcy Tirrel discovered frozen dinosaur corpses in the Arctic.
In 17,000 B.C., the Seven Primes traveled the galaxy to create Energon with star-absorbing machines called Sun Harvesters. The Primes followed a rule in which to never destroy planets with life, but one of them, later called The Fallen, deceives the others by building an army and sets up a Harvester on Earth. After defeating ancient humans, the Primes defeat and imprison the Fallen before he can harvest the Earth's sun with the Matrix of Leadership. The rest of the Primes sacrifice themselves to hide the Matrix.
On July 2, a 500 km wide alien mothership enters Earth's orbit and deploys several dozen saucer-shaped "destroyer" spacecraft, each 15 miles (24 km) wide. As they take position over some of Earth's major cities, David Levinson (Jeff Goldblum), an MIT graduate working for a cable company in New York City, discovers hidden transmissions in Earth's satellites which he realizes is a timer counting down to a coordinated attack by the aliens. With the support of his estranged wife Constance Spano (Margaret Colin), the White House Communications Director, he and his father Julius (Judd Hirsch) gain entrance into the Oval Office to notify President Thomas J. Whitmore (Bill Pullman) about the attack. Whitmore orders large-scale evacuations of the targeted cities, but the aliens attack with advanced directed-energy weapons before these can be carried out. Whitmore, portions of his staff, and the Levinsons narrowly escape aboard Air Force One as Washington, D.C. is destroyed.
Many years ago, the planet Cybertron was consumed by a civil war by the two Transformer factions, the Autobots led by Optimus Prime, and the Decepticons led by Megatron. Optimus jettisoned the AllSpark, a mystical artefact that brings life to the planet, into space, but Megatron pursued it. Megatron crashed in the Arctic Circle and froze, discovered in 1897 by explorer Archibald Witwicky. Witwicky activated Megatron’s navigational system, which scanned the AllSpark’s coordinates into his glasses. The glasses end up in the possession of his great-great-grandson Sam Witwicky. In the present day, Sam buys his first car, a rusting Chevrolet Camaro, but discovers it has a life of its own.
The planet Krypton faces imminent destruction due to its unstable core; the result of depleting Krypton's natural resources. The ruling council is deposed by the planet's military commander, General Zod, and his followers during a coup d'état. Knowing that artificial population control and isolationism have ruined their civilization, scientist Jor-El and his wife Lara launch their newborn son, Kal-El, the first naturally born Kryptonian child in centuries, on a spacecraft to Earth after infusing his cells with a genetic codex of the entire Kryptonian race. After Zod kills Jor-El, he and his followers are captured and exiled to the Phantom Zone. However, they are indirectly freed after Krypton explodes, rendering the Kryptonian race extinct apart from Zod and his forces.
The narrator (Morgan Freeman) explains how humans were unaware that intelligent extraterrestrials were making plans to occupy Earth. Ray Ferrier (Tom Cruise) is a divorced crane operator longshoreman who works at a dock in Bayonne, NJ. Ray is estranged from his children. His former wife, Mary Ann (Miranda Otto), later drops off the children, 10-year-old daughter Rachel (Dakota Fanning) and teenage son Robbie (Justin Chatwin), at Ray's house in Bayonne on her way to visit her parents in Boston. Unexplained changes in the weather occur, emitting lightning that strikes multiple times in the middle of an intersection and disrupting all electrical technology in the area.
The Hess family lives on an isolated farm in Doylestown, Bucks County, Pennsylvania. Graham Hess (Mel Gibson) is a former priest whose wife, Colleen, died in a horrific traffic accident caused by a town local, Ray Reddy (Shyamalan). No longer practicing religiously, Graham lives with his asthmatic son, Morgan (Rory Culkin), daughter Bo (Abigail Breslin), who leaves water glasses all over the house because of various reasons, and Graham's younger brother, Merrill (Joaquin Phoenix), a former minor league baseball star who never made it to the major leagues because he swung too hard and struck out too often. Graham discovers a huge crop circle in his field, reports of violent animal behavior have spread across town, and one of the Hess' dogs tries to attack Bo and Morgan, forcing them to kill it.
In 2013, Earth's coastal cities come under attack from Kaijus, colossal beasts that periodically emerge from a dimensional portal on the Pacific Ocean floor called "The Breach." To fight them, the Pacific Rim nations build the Jaegers, equally colossal humanoid war machines. Each Jaeger is controlled by two or more pilots whose brains are linked, called "drifting" to share the heavy mental load of operating the machine. The Jaegers are initially effective, but many are destroyed as the Kaijus grow more powerful and their attacks become more frequent. In 2025, the participating governments deem the Jaeger program unsustainable and discontinue it in favor of building defensive coastal walls. The four remaining Jaegers are redeployed to Hong Kong to protect the coast until the walls are completed. Jaeger commander Stacker Pentecost resolves to make a last-ditch attempt to end the Kaiju threat by destroying The Breach with a nuclear weapon, even though past nuclear strikes on the portal have been unsuccessful.
A race of extraterrestrials called Mimics has taken over continental Europe. In England, General Brigham, head of humanity's United Defense Force, orders Major William Cage, a public affairs officer with no combat experience, to cover the next day's amphibious assault in France. Cage objects to the dangerous assignment and threatens to blackmail Brigham to avoid it. Brigham has Cage arrested; Cage is knocked out trying to escape. He wakes in handcuffs at a forward operating base at Heathrow Airport and discovers he has been demoted to private, charged with desertion, and assigned to a combat squad named "J" squad under the command of Master Sergeant Farell.
In 2005, scientists discover an extrasolar planet, which they name Planet G, with conditions similar to Earth. In 2006 NASA transmits a powerful signal from a communications array in Hawaii. Meanwhile, slacker Alex Hopper gets arrested while attempting to impress Sam Shane, daughter of U.S. Pacific Fleet commander Admiral Terrance Shane. Stone Hopper, Alex's older brother and a naval officer, is infuriated at Alex's lack of motivation and forces Alex to also sign up and earn a commission in the U.S. Navy.
In 2077, the Earth has been devastated by war with an extraterrestrial invader, the Scavengers (Scavs). Humanity is relocating to Saturn's moon Titan via the Tet, a large tetrahedron-shaped space station. Gigantic offshore fusion energy generators drain the oceans to produce power for the colonists on Titan.
In the summer of 1982, Sam Brenner and Will Cooper are thirteen-year-olds who love playing in the local arcade. Brenner enters an arcade game world championships. At the event, the MC tells that a time capsule will be launched into space containing a videocassette that includes scenes from the championships. Brenner and Cooper meet Ludlow Lamonsoff, a child who's in love with Lady Lisa, the main character of the game Dojo Quest. Brenner succeeds in every game, but finally loses to Eddie Plant in Donkey Kong.