Shortly after the events of Jurassic World, a small team of mercenaries arrives on the abandoned Isla Nublar to collect DNA from the remains of the Indominus rex at the bottom of the park’s lagoon. After successfully collecting a bone fragment, the team’s survivors barely escape the island following attacks by the Mosasaurus and Tyrannosaurus rex.
Three years later in 2018, a U.S. Senate hearing in Washington, D.C. debates whether Isla Nublar’s dinosaurs should be saved from an impending volcanic eruption. Mathematician Dr. Ian Malcolm testifies that the dinosaurs should be allowed to perish to correct John Hammond’s mistake of cloning them. Meanwhile, Jurassic World’s former operations manager, Claire Dearing, has created the Dinosaur Protection Group to save the animals. After the Senate rules against rescuing the dinosaurs, Hammond’s former partner, Benjamin Lockwood, summons Claire to his Northern California estate. Lockwood and his aide, Eli Mills, reveal a plan to relocate the dinosaurs to a new island sanctuary. Claire is needed to help reactivate the park’s dinosaur tracking system to locate the animals, particularly Blue, the last living Velociraptor. Although they are estranged, Claire recruits Jurassic World’s former Velociraptor trainer and Blue’s alpha, Owen Grady, to help capture her.
On Isla Nublar, Claire and former park technician Franklin Webb get the tracking system online. Owen, paleo-veterinarian Zia Rodriguez, and a mercenary team led by Ken Wheatley search for Blue. Upon finding her, the encounter escalates, resulting in a mercenary shooting Blue and Wheatley tranquilizing Owen. The mercenaries take Zia so she can treat Blue’s injury. Their ship departs for the U.S. mainland as the animals left behind die in the eruption. Claire, Franklin, and Owen sneak aboard in time and assist Zia in transfusing Blue with Tyrannosaurus blood. The group now realize the captured dinosaurs were never being transported to a new island and are for another purpose.
Back at the estate, Lockwood’s orphaned pre-teen granddaughter Maisie overhears Mills and auctioneer Gunnar Eversol secretly planning to auction the captured dinosaurs on the black market. They will also unveil the Indoraptor, a new genetically-engineered dinosaur created by geneticist Dr. Henry Wu using Indominus rex and Velociraptor DNA. Wu wants Blue’s DNA to create an enhanced Indoraptor, unaware that Blue’s blood is contaminated. After Maisie informs Lockwood about the auction, he confronts Mills, who murders him. Maisie is later revealed to have been cloned from Lockwood’s deceased daughter and is the reason John Hammond, who opposed human cloning, ended their partnership.
The dinosaurs are transported to Lockwood’s estate and caged. Zia and Franklin evade capture, but Owen and Claire are apprehended and confined. Owen incites a Stygimolochinto breaking open their cell. They find Maisie who leads them to the auction where the Indoraptor is being sold despite Wu’s protests that it is a prototype. Owen disrupts the proceedings by luring the Stygimoloch into the room. In the ensuing chaos, Wheatley tranquilizes the Indoraptor to extract a tooth as a trophy, but it feigns sedation and escapes, killing him, Eversol, and others. The Indoraptor hunts Owen, Claire, and Maisie throughout the mansion. Zia releases Blue, who attacks the Indoraptor, causing it to fall through a glass roof to its death.
When a hydrogen cyanide gas leak threatens the caged animals, Maisie is unable to let them die and frees them despite Owen’s warning. Mills is killed and the Indominus bone destroyed by the Tyrannosaurus. Owen, Claire, Maisie, Zia, and Franklin safely get away, while Blue and the other dinosaurs escape.
In a new U.S. Senate hearing, Dr. Malcolm declares the beginning of a Neo-Jurassic Age where humans and dinosaurs must learn to coexist. The closing scenes show the freed dinosaurs roaming wilderness and outer urban areas.