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.
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.
In 1954, a nuclear bomb is detonated at the moment a giant creature emerges from the ocean. In 1999, Project Monarch scientists Ishiro Serizawa and Vivienne Graham investigate a colossal skeleton unearthed in a collapsed mine in the Philippines. They find two spores; one dormant and one hatched that made a trail into the sea. In Japan, the Janjira Nuclear Power Plant experiences unusual seismic activity and Supervisor Joe Brody sends his wife Sandra and a team of technicians into the reactor. A tremor breaches the reactor, leaving Sandra and her team unable to escape while the plant collapses.
In 1995, John Connor is ten years old and living in Los Angeles with foster parents. His mother Sarah Connor had been preparing him throughout his childhood for his future role as the leader of the Human Resistance against Skynet, but was arrested after attempting to bomb a computer factory and imprisoned at a mental hospital under the supervision of Dr. Silberman. Skynet sends a new Terminator, designated as T-1000, back in time to kill John. The T-1000 is an advanced prototype composed of a mimetic polyalloy that allows it to take on the shape and appearance of almost anything it touches, and transform parts of its anatomy into knives and other stabbing weapons. The T-1000 arrives under a freeway, kills a policeman and assumes his identity. Meanwhile, the future John Connor has sent back a reprogrammed T-800 (Model 101) Terminator to protect his younger self.
In 1912, 13-year-old Indiana Jones is horseback riding with his Boy Scout troop in Moab, Utah. While scouting caves, Indy discovers a group of grave robbers who have found a golden crucifix belonging to Coronado and steals it from them, hoping to donate it to a museum. The men give chase through a passing circus train, leaving Indy with a bloody cut across his chin from a bullwhip and new phobia of snakes. Indy escapes, but the local sheriff makes him return the crucifix. Impressed with Indy's bravery, the leader of the robbers gives Indy his fedora.
In 2029, Human Resistance leader John Connor (Jason Clarke) launches a massive final offensive against Skynet, an artificial general intelligence system seeking to eliminate the human race. Before the Resistance wins the offensive, Skynet activates a time machine and sends back a T-800 Terminator to 1984 to kill John's mother, Sarah Connor (Emilia Clarke). John's right-hand man, Kyle Reese (Jai Courtney), volunteers to travel back in time to protect her. As Kyle floats in the machine's magnetic field, he witnesses John being attacked by another Resistance soldier (Matt Smith). He then has visions from his childhood about events in 2017.
John Connor has been living off the grid in Los Angeles in the years following the death of his mother, Sarah, from leukemia. Although Judgment Day did not occur on August 29, 1997, as expected, John still believes that a war between humans and the machines will occur. Unable to locate John in the past, Skynet sends a new model of the Terminator called the T-X back to July 24, 2004 to kill other members of the Human Resistance. The T-X is more advanced than previous Terminators, and has an endoskeleton with built-in weaponry, a liquid metal exterior similar to the T-1000, and the ability to reprogram other machines. Unlike previous Terminators, its standard appearance is female. The Resistance sends a reprogrammed Terminator (T-850 - Model 101) back in time to protect the T-X's targets including John and his future wife, Kate Brewster.
Teenager Marty McFly is an aspiring musician dating girlfriend Jennifer Parker in Hill Valley, California. His father George is bullied by his supervisor, Biff Tannen, while his mother Lorraine is an overweight, depressed alcoholic. Whilst expressing disapproval of Marty's relationship with Jennifer, Lorraine recounts how she met George when her father hit him with a car.
In 2003, Dr. Serena Kogan (Helena Bonham Carter) of Cyberdyne Systems convinces death row inmate Marcus Wright (Sam Worthington) to sign over his body for medical research following his execution. One year later, the automated Skynet system is activated, begins to perceive humans as a threat, and eradicates much of humanity with nuclear weapons in the event known as "Judgment Day".
In 1944, in a German concentration camp in occupied Poland, Nazi scientist Dr. Klaus Schmidt witnesses a young Erik Lensherr bend a metal gate with his mind when the child is separated from his mother. In his office, Schmidt orders Lensherr to move a coin on his desk, and kills the boy's mother when Lensherr cannot. In grief and anger, Lensherr's magnetic power manifests, killing two guards and destroying the room. Meanwhile, at a mansion in Westchester County, New York, child telepath Charles Xavier meets young shapeshifter Raven, whose natural form is blue-skinned and scaly. Overjoyed to meet someone else "different", he invites her to live with his family as his foster sister.
Slate and Co. Senior Executive Cliff Vandercave (Kyle MacLachlan) and secretary Miss Sharon Stone (Halle Berry) look at the company workers in the gravel pits while discussing their plan to swindle the company of its vast fortune and flee, but decided that they need someone to take responsibility for it. Fred Flintstone (John Goodman) loans his best friend and neighbor Barney Rubble (Rick Moranis) money so that he and his wife Betty (Rosie O'Donnell) can adopt a child named Bamm-Bamm, who can only pronounce his own name. Although the child is initially difficult to control due to being raised by Mastadons, as well as being superstrong, he eventually warms up to his new family. Barney vows to repay his friend, but Fred is visited by his mother-in-law, Pearl Slaghoople (Elizabeth Taylor), who objects to his decision. However, Fred's wife Wilma (Elizabeth Perkins) remains supportive of his decision.
On October 5, 1985, Dr. Emmett "Doc" Brown arrives in his flying time machine and persuades Marty McFly and his girlfriend, Jennifer Parker, to come back to the future with him to help their future children. Biff Tannen witnesses their departure. They arrive on October 21, 2015, where Doc electronically knocks out Jennifer and leaves her asleep in an alley, explaining that she should not have too much knowledge of future events. He has Marty pose as his own son to refuse an offer to participate in a robbery with Biff's grandson, Griff.
In an alternate timeline in which Earth was never hit by an asteroid and dinosaurs never became extinct, a young Apatosaurus named Arlo loses his father in a tragic accident. One day, Arlo falls into a river and gets knocked out by a rock, finding himself far away from his home. While trying to find a way back to the Clawed-Tooth Mountains, he befriends a human caveboy that he names Spot.