Six months following the catastrophic events at Jurassic World on Isla Nublar, a group of mercenaries ventures into the deserted island with the goal of retrieving DNA from the remains of the Indominus Rex, which lie submerged at the bottom of the park's lagoon. After successfully collecting a bone fragment, they narrowly escape the wrath of the park's menacing Mosasaurus and Tyrannosaurus Rex. In the chaos of their evacuation, the lagoon gate is inadvertently left ajar, enabling the Mosasaurus to swim freely into the ocean.
Fast forward three years, a U.S. Senate hearing in Washington, D.C. debates the fate of the dinosaurs on Isla Nublar in light of an impending volcanic eruption. Dr. Ian Malcolm (Jeff Goldblum), a noted mathematician and chaos theory expert who previously consulted for InGen's Jurassic Park, passionately argues that the dinosaurs should be allowed to perish in order to rectify John Hammond's historical error of cloning them. Meanwhile, Claire Dearing (Bryce Dallas Howard), the former operations manager at Jurassic World, founds the Dinosaur Protection Group to advocate for the salvation of these creatures. When the Senate ultimately votes against rescuing the dinosaurs, Claire receives a call from Benjamin Lockwood (James Cromwell), Hammond's erstwhile partner in dinosaur cloning technology.
Claire soon finds herself at Lockwood's Northern California estate, where he and his aide, Eli Mills (Rafe Spall), share a bold plan to relocate the dinosaurs to a new sanctuary island. With concerns specifically about tracking down Blue, the last remaining Velociraptor, Mills enlists the help of Owen Grady (Chris Pratt), the former Velociraptor trainer, for their ambitious mission.
Upon their arrival at Isla Nublar, they connect with Ken Wheatley (Ted Levine), the mercenary leader. Together, Claire and former park technician Franklin Webb (Justice Smith) reactivate the dinosaur tracking system while Owen, Paleo-veterinarian Zia Rodriguez (Daniella Pineda) and the mercenaries initiate the search for Blue. However, things take a drastic turn as a militant member of the team fires a shot at Blue, during which Owen is tranquilized. Zia bravely fights to keep Blue alive as Owen grapples with the distressing events. Following a close encounter with a Baryonyx, Claire and Franklin manage to reunite with Owen as the volcanic eruption wreaks havoc across the island. They escape the devastation just in time, sneaking onto the mercenaries' ship, where they discover Zia has managed to keep Blue safe. As they set sail for the United States, Isla Nublar is left engulfed in flames, ushering the last of its dinosaurs to their demise.
Back at Lockwood's estate, his young granddaughter Maisie ([Isabella Sermon]) inadvertently overhears a clandestine meeting between Mills and auctioneer Gunnar Eversol (Toby Jones), who are scheming to sell the captured dinosaurs to the highest bidder. Mills, motivated by greed, plans to utilize the auction proceeds to fund the development of a genetically engineered species known as the Indoraptor, crafted using the DNA of both the Indominus Rex and a Velociraptor, with the assistance of geneticist Dr. Henry Wu (BD Wong). When Maisie informs Lockwood of the auction, it spirals into tragedy as Mills turns on Lockwood, ending his life.
As the dinosaurs are brought to Lockwood's estate and caged, Zia and Franklin manage to evade capture, while Owen and Claire find themselves imprisoned. Utilizing a Stygimoloch's strength, Owen ingeniously breaks free from their containment. They cross paths with Maisie, who guides them to the live auction of the Indoraptor, despite Wu's insistence that it is merely a prototype. In an effort to reclaim control, the freed Stygimoloch, under Owen's direction, wreaks havoc on the auction house. In the ensuing chaos, after being tranquilized, the Indoraptor pulls a shocking twist, feigning sedation and slaying Wheatley, Eversol, and several others present.
In a shocking revelation, Mills discloses to Owen and Claire that Maisie is actually a clone of Lockwood's late daughter, a fact that drove a wedge between Hammond and Lockwood, forcing them apart. The Indoraptor becomes the unwitting predator, hunting Owen, Claire, and Maisie throughout the mansion. Just when things seem dire, Zia releases Blue, prompting a fierce showdown which ends with the Indoraptor plummeting to its death through the mansion's glass roof.
As tensions rise, a hydrogen cyanide gas leak looms, prompting Maisie to act against Owen's caution and liberate the imprisoned dinosaurs, refusing to allow them to perish. Mills, in a desperate attempt to escape with a bone from the Indominus Rex, meets a gruesome end as he falls prey to the Tyrannosaurus and Carnotaurus. Ultimately, Owen and Claire escape the estate with Maisie, while Blue and the other dinosaurs find freedom. In a newly convened U.S. Senate hearing, Dr. Malcolm asserts the imperative for humans and dinosaurs to learn to coexist in this new world.
The film concludes with a poignant scene, showing the dinosaurs reclaiming their place in both wilderness and urban environments.
