Incidents surrounding Isla Sorna don't deter tourists Ben Hildebrand and Eric Kirby from para sailing around the island despite warnings, but when their boat crashes, Ben cuts them from their line and they go sailing into the wilderness.
Meanwhile, Dr. Alan Grant, Thomas, Percy, James, Toby, Emily, Gordon, Henry, Edward, Bash, Dash, Ferdinand, Luke, Charlie, Hiro, Victor, Kevin, Skarloey, Rheneas, Sir Handel, Peter Sam, Rusty, Duncan, Twilight Sparkle, Applejack, Pinkie Pie, Fluttershy, Rainbow Dash, Rarity, the CMC, Spike, Shining Armor, Princess Cadence, Zecora, Stephen, Steamy, Puffy, Evan, Shai-Shay, T.C., Hugs, Buzz, J.J., Sharky, Mako, Willy, The Miner Trains, and Rattlesnake Jake have become famous from their survival and reporting of their discoveries on Isla Nublar, and Ellie Sattler, never marrying Alan, is married to lawyer Mark Delger and has a son Charlie, who calls Alan "The Dinosaur Man." One afternoon, Alan's assistant Billy is able to replicate the larynx of a Velociraptor which he says indicates raptors are far more intelligent than Alan and Billy had previously been led to believe. Being approached by a couple, Paul and Amanda Kirby, who offer full funding for their dig, Alan and the others hesitantly agree to give them an aerial tour of Isla Sorna, and Billy attends. With the Kirbys' associates, Udesky, Cooper and their pilot Nash, Alan and our heroes learn that they plan to land on the island. When Alan objects, he is knocked out by Cooper, only to awaken to the sound of Amanda calling out to someone on the island using a bullhorn. This attracts a Spinosaurus and Cooper manages to lead it into the path of the plane before he is devoured. The plane then crashes into a tree and the Spinosaurus attacks the plane, killing Nash. The Spinosaurus soon leaves and the others escape. As they continue to escape, a Tyrannosaurus appears and the humans escape in the fray before the Spinosaurus manages to snap the T. rex's neck. After finding Ben's remains in a para sail trapped in a tree and seeing a video of his and Eric's final descent onto the island, the Kirbys explain they're actually a divorced couple looking for their son, Eric. Their fortune is fake, and Alan's grim perspective of Eric's fate paints a sad portrait; Udesky and Grant, Willy, and Scootaloo become separated from the others when they're attacked by Velociraptors and Udesky is killed by them after being used as live bait, proving their intelligence. Alan, Willy, and Scootaloo are rescued by Eric, who has managed to survive for several weeks in an overturned supply truck, clearly impressing Alan. Eric recognizes the sound of his father's satellite phone which was lost when Nash was eaten; they're reunited with the Kirbys, the other engines and ponies, zebra, and Billy before the Spinosaurus attacks again. Narrowly escaping, they make their way to the site compound in the hopes of finding communications equipment, but find nothing but broken test tubes and shut down equipment.
Billy becomes possessive of his satchel, and when Alan looks he realizes Billy had taken two eggs from the raptors' nest to fund for their dig, while Fluttershy sternly asks Willy to give her saddlebags back, and when Willy looks, he finds stolen Raptor eggs in Fluttershy' saddlebags too explaining the reason they were being attacked. Alan berates Billy for his careless behavior, comparing him to nothing more than InGen. Everyone else is outraged that Fluttershy put their lives in jeprody for stupid eggs, and Mako literaly struggles Fluttershy for what she did. Mako then furiously tells Fluttershy that's she a walking death trap (even bringing up her causing the parasprite invasion, destroying the Grand Galloping Gala, and betraying Twilight, Thomas, and Percy at Shining Armor and Cadance's wedding.) and Rattlesnake Jake claims that's she's the biggest coward that he ever met. They make their way to a large outdoor complex which turns out to be a bird cage for a Pteranodon which attack the group and separates Eric and Fluttershy, taking them to be eaten by their young. Billy uses the remnants of Ben's para sail and rescues Eric, while Willy jumps into the nest and fights the young Pteranodons and kills them with his diamond dagger and Billy shortly falls into the river below, then is attacked and seemingly killed by a group of Pteranodons.
The group find their way out of the cage and make their way down river using a small boat. Alan is shocked by Billy's 'death', and explains to Eric that Billy was a person who wanted to do something, not just sit by and watch, using the example of being an astronaut instead of an astronomer. The group finds and retrieves the satellite phone from the deposit left by the Spinosaurus. It attacks and capsizes the boat as Alan is trying to contact Ellie, but he manages to tell her "The River, Site B" before he's disconnected. Alan and Paul manage to drive off the Spinosaurus, while Mako attacks it and tears off it's left arm then Steamy lights a stick of dynamite and then makes the Spinosaurus eat it, which blows it up; killing it and they start making their way toward the shoreline. Close to their goal, they're surrounded by raptors who see Amanda as a female 'leader' and a threat to their clutch. Using Billy's resonant chamber replica, Alan manages to communicate with the raptors and Amanda returns the stolen eggs and Rarity forces Fluttershy to give back the eggs she stole (By threatening never to go with the spa with her ever again.) before they're startled off by the sounds of helicopters. Returning to the beach, they find that Ellie had called in the U.S. Marine Corps and the U.S. Navy to rescue them. And they discover that Billy, while badly wounded, is still alive, and even has Alan's hat, which he had lost earlier. As they depart the island, they see the Pteranodon group that had escaped from their cage after the humans are now flying free, and Alan recounts that it's time for them to find their place in the world again. The Pteradons fly off into the clouds, seemingly happy of being freed of their cage.
- Stephen, Zecora, Steamy, Puffy, Evan, Shai-Shay, Sharky, Willy (the train), the Miner Trains (Steam Grindor, Steam Mech, Mucker, Steam Claw D., Steam Driller, Steam Sweeper, and Steam Exavator), T.C., Hugs, Buzz, J.J., Mako, and Rattlesnake Jake will guest star in this film.
- Fluttershy will also steal Raptor eggs because she wanted to take them home and make them her pets and train them to be her bodyguards when they grow up.
- This film will be dedicated to Michael Jeter, who had died after suffering an epileptic seizure.
- The storyline concludes in Thomas and Twilight Sparkle visit Jurassic World.
- Isla Sorna
- The dinosuar man
- The dig site
- Kirby's proposition
- The Spinosaurus
- T-Rex vs. Spinosaurus
- Explaination/Discovering the Parasail
- Raptor Eggs/InGen Laboratory
- Eric/in the trees
- Reunited/Finding the stolen eggs
- The Pteradons cage
- On the river/finding the phone
- The Spinosarus attacks/killing the beast
- Returning the eggs/rescued/Princess Celestia's resoning with Fluttershy