In 1996, treasure hunter Brock Lovett and his team aboard the research vessel Akademik Mstislav Keldysh search the wreck of RMS Titanic for a necklace with a rare diamond, the Heart of the Ocean. They recover a safe containing a drawing of a young woman wearing only the necklace dated April 14, 1912, the day the ship struck the iceberg. Rose Dawson Calvert, the woman in the drawing, is brought aboard Keldysh and tells Lovett of her experiences aboard Titanic.
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.
After a failed attempt to rescue his first mate, Joshamee Gibbs, in London, Captain Jack Sparrow is brought before King George II, who wants Jack to guide an expedition to the Fountain of Youth before King Ferdinand and the Spanish Navy can locate it. Heading the expedition is Jack's old nemesis, Captain Hector Barbossa, now a privateer in service to the British Navy after losing his leg and ship, the Black Pearl, which he believes to be sunk.
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.
In 2009, American geologist Adrian Helmsley visits astrophysicist Satnam Tsurutani in India and learns that neutrinos from a massive solar flare are causing the temperature of the Earth's core to rapidly increase. Arriving at a party in Washington, D.C, Helmsley presents his information to White House Chief of Staff Carl Anheuser, who takes him to meet the President.
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.
In the future, robots known as Sentinels are exterminating mutants and their human allies. A band of mutants, including Kitty Pryde, Colossus, Iceman, Bishop, Warpath, Blink and Sunspot, evade the Sentinels due to Pryde's ability to send a person's consciousness to the past. Pryde's group convenes with Logan, Storm, Professor Charles Xavier, and Erik Lehnsherr at a monastery in China. Pryde sends Logan's consciousness 50 years back in time to 1973 to prevent Mystique from assassinating Dr. Bolivar Trask, creator of the Sentinels. Following the assassination, Mystique was captured, and her DNA was used by Trask's company to improve the Sentinels, whose ability to adapt to any mutant power makes them almost invincible. Xavier and Lehnsherr advise Logan to find both of their younger selves for help.
Six months after the events of the first film, Neo and Trinity are now lovers. Morpheus receives a message from Captain Niobe of the Logos calling an emergency meeting of all of Zion's ships. Zion has confirmed the last transmission of the Osiris: an army of Sentinels is tunneling towards Zion and will reach it within 72 hours. Commander Lock orders all ships to return to Zion to prepare for the onslaught, but Morpheus asks one ship to remain in order to contact the Oracle. The Caduceus receives a message from the Oracle, and the Nebuchadnezzar ventures out so Neo can contact her. One of the Caduceus crew, Bane, encounters Agent Smith, who takes over Bane's avatar. Smith then uses this avatar to leave the Matrix, gaining control of Bane's real body.
Dr. Ryan Stone (Sandra Bullock) is a biomedical engineer aboard the NASA space shuttle Explorer for her first space mission, STS-157. Veteran astronaut Matt Kowalski (George Clooney) is commanding his final mission. During a spacewalk to service the Hubble Space Telescope and Stone's upgrades to the Telescope, Mission Control in Houston warns the team about a Russian missile strike on a defunct satellite, which has inadvertently caused a chain reaction forming a cloud of debris in space. Mission Control orders that the mission be aborted and the crew begin re-entry immediately because the debris is speeding towards the shuttle. Communication with Mission Control is lost shortly thereafter.
Ten years after the worldwide pandemic of the deadly ALZ-113 virus (known as the Simian Flu), human civilization is completely destroyed following martial law, civil unrest and the economic collapse of every country in the world. Over 90% of the human population has died in the pandemic, while apes with genetically enhanced intelligence have started to build a civilization of their own.
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.
Crop blight has made growing food on Earth nearly impossible, threatening the existence of humanity. Joe Cooper, a widowed former NASA pilot, runs a farm with his father-in-law Donald, son Tom, and daughter Murphy. Murphy believes her bedroom is haunted by a poltergeist. When the "ghost" creates a pattern of dust on the floor, Cooper realizes an unknown intelligence is using gravity to communicate, and interprets the pattern as geographic coordinates, which Cooper and Murphy follow to a secret NASA installation.