Two decades after the events at Jurassic Park, a new theme park, Jurassic World, now operates in Isla Nublar, off the Pacific coast of Central America. This new park is run by the Masrani Global Corporation, which also owns InGen, the genetics company that creates the dinosaurs. Brothers Zach and Gray Mitchell are sent to visit their aunt, Claire, Jurassic World's operations manager. Claire's assistant greets them as she is too busy recruiting corporate sponsors.
John Hammond, the founder and CEO of bioengineering company InGen, has created a theme park called Jurassic Park on Isla Nublar, a tropical island populated with cloned dinosaurs. After a park worker is killed by a Velociraptor, the park's investors, represented by lawyer Donald Gennaro, demand that experts visit the park and certify it as safe. Gennaro invites the mathematician Ian Malcolm while Hammond invites paleontologist Dr. Alan Grant and paleobotanist Dr. Ellie Sattler. Upon arrival, the group is stunned to see three Brachiosaurus and a herd of Parasaurolophus in the distance.
Peter Parker plans to propose to Mary Jane Watson, who has just made her Broadway musical debut. A meteorite crashes near the two in Central Park, and an extraterrestrial symbiote attaches itself to Peter's moped. While fleeing police, escaped prisoner Flint Marko falls into a particle accelerator that fuses his DNA with surrounding sand, allowing him to shapeshift at will as the Sandman. Peter's best friend, Harry Osborn, who blames him for his father's death, attacks Peter using weapons based on his father's Green Goblin technology. Harry injures his head and suffers partial amnesia, forgetting that Peter is Spider-Man and his desire for revenge. During a festival honouring Spider-Man, Marko robs an armored car. NYPD Captain George Stacy tells Peter and Aunt May that Marko was Uncle Ben's killer, and Dennis Carradine was only an accomplice. While a vengeful Peter sleeps, the symbiote bonds with him. Peter wakes up hanging from a skyscraper. His costume becomes black and his powers increase, but the symbiote brings out Peter's dark side. Wearing the new suit, Spider-Man locates Marko and battles him in a subway tunnel, reducing him to mud using water.
High-school senior Peter Parker visits a genetics laboratory with his friend Harry Osborn and love interest, Mary Jane Watson for a school field trip. There, Peter is bitten on the hand by a genetically engineered "super spider". Shortly after arriving home to his Aunt May and Uncle Ben, he goes unconscious. Meanwhile, Harry's father, scientist Norman Osborn, owner of Oscorp, is attempting to preserve his company's critically important military contract. He experiments on himself with a new but unstable performance-enhancing chemical vapor that increases his speed, strength, and stamina. However, it also drives him insane and he kills his assistant, Mendel Stromm. The next morning, Peter finds that his previously impaired vision has improved and his body has metamorphosized into a more muscular physique. At school, he finds that his body can produce webs and his quickened reflexes let him avoid injury during a confrontation with bully Flash Thompson. Peter discovers he has developed superhuman speed, strength, the ability to stick to surfaces, and a heightened ability to sense danger.
Peter Parker struggles to balance his crime-fighting duties as Spider-Man with the demands of his normal life. He loses a job, faces financial difficulties, and struggles to attend his physics lectures at Columbia University on time. Estranged from both love interest Mary Jane Watson and best friend Harry Osborn, who intends to seek revenge on Spider-Man for his father Norman's death, Peter additionally discovers his Aunt May is facing foreclosure.
A young Peter Parker discovers his father Richard Parker's study has been burgled. Gathering up hidden documents, Peter's parents take him to the home of his Aunt May and Uncle Ben, then mysteriously depart.
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.
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.
OsCorp scientist Richard Parker records a video message to explain his disappearance. Later, he and his wife, Mary, are aboard a private jet hijacked by a man sent to assassinate Richard. The plane crashes, killing both Richard and Mary, after he uploads the video.
Four years after the disaster at Jurassic Park, the wealthy Bowman family makes an excursion to the island of Isla Sorna during a yachting cruise. Their young daughter wanders off and is attacked by a pack of Compsognathus, but survives. The incident allows Peter Ludlow, John Hammond's nephew, to gain control of his uncle's company InGen, which is in severe financial straits after the events at Jurassic Park. Hammond contacts Ian Malcolm and explains that Isla Sorna is the island where the dinosaurs were engineered and nurtured before being moved to Isla Nublar, Jurassic Park's location. He also explains that after the park was shut down, Isla Sorna was abandoned during a hurricane and the dinosaurs left to survive in the wild, where they have been inexplicably thriving. Hammond asks Malcolm to join a team that will travel to Isla Sorna to document the dinosaurs in order to rally public support against human interference on the island. Ian initially declines but, after learning that his girlfriend, paleontologist Sarah Harding, is part of the team and is already on the island, he agrees to go.
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.
Will Rodman, a scientist at the biotechnology company Gen-Sys, is testing viral-based drug ALZ-112 on chimpanzees to find a cure for brain ailments such as Alzheimer's disease. The drug is given to a chimpanzee, Bright Eyes, greatly increasing her intelligence. However, when Will is presenting 112 to his boss and uses Bright Eyes as an example, she is forced from her cage, goes on a rampage, and is killed. Will's boss Steven Jacobs terminates the project and orders chimp handler Robert Franklin to euthanize the chimps. After doing as ordered, Franklin discovers that Bright Eyes had recently given birth and understands the reason why she was disturbed. He convinces Will to save the baby chimp's life by taking him home temporarily. Will's father Charles, who is suffering from Alzheimer's, names the chimp "Caesar", in reference to William Shakespeare's play Julius Caesar, from which he can, despite his deteriorating mental condition, cite long passages from memory. Will learns that Caesar has inherited his mother's high intelligence (the 112 virus passing to him in utero) and decides to raise him, working from home and observing his behavior in hopes that he can get the project restarted. Three years later, Will introduces Caesar to the redwood forest at Muir Woods National Monument. Meanwhile, with Charles' condition rapidly deteriorating, Will treats him with ALZ-112 and he is restored to better-than-original cognitive ability.
An infamous hacker called Trinity (Carrie-Anne Moss) is cornered in an abandoned hotel by police. She easily overpowers and escapes from them, but a group of sinister black-suited Agents with superhuman abilities lead the police in a rooftop pursuit after her. Upon picking up a ringing phone in a telephone booth, she vanishes without a trace.
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.