John Hammond, the founder and CEO of bioengineering company InGen, has created on Isla Nublar, a tropical island near Costa Rica, a theme park called Jurassic Park, populated with cloned dinosaurs. After a park worker is killed by a Velociraptor, the park's investors, represented by the 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, paleobotanist Dr. Ellie Sattler and 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, Spike, the CMC, Shining Armor and Princess Cadence (who also bring Zecora and Stephen). Upon arrival on Isla Nublar, the group and all our heroes are stunned to see a Brachiosaurus and a herd of Parasauolophus in the distance.
On the visitor center, the crew learns through an explanatory video and a tour through a laboratory that the cloning was accomplished by extracting the DNA of dinosaurs from mosquitoes that had been preserved in amber. However, the strands of DNA were incomplete, so DNA from frogs were used fill in the gaps. The dinosaurs all were cloned genetically as females in order to prevent breeding.
The group and all our heroes are then joined by Hammond's grandchildren, Lex and Tim Murphy (and along with Steamy, Puffy, Shai-Shay, Evan, T.C., Hugs, Buzz, J.J., Sharky, Willy, Rattlesnake Jake and the Miner Trains (Steam Grindor, Steam Mech, Mucker, Steam Claw D., Steam Driller, Steam Sweeper, and Steam Exavator) for a tour of the park, while Hammond oversees the trip from the park's control room. However, the tour does not go as planned, with most of the dinosaurs failing to appear and a Triceratops becoming ill. As a tropical storm approaches Isla Nublar, most of the park employees depart on a boat for the mainland and the visitors returns to the electric tour vehicles except Ellie, Victor, and Zecora, who stay with the park's veterinarian to study the Triceratops.
During the storm, Jurassic Park's computer programmer, Dennis Nedry, who has secretly been paid by a corporate rival to steal dinosaur embryos, deactivates the park's security system to allow him access to the embryo storage room. Most of the park's electric fences are deactivated, leading the Tyannosaurus to attack the tour group. Grant, Lex, Tim, Stephen, the CMC, Spike, Mako, Willy, The Miner Trains, and Shai-Shay narrowly escape while the T. rex devours Gennaro. The T-Rex injures Malcolm and causes the rest of the team to get stuck under rumble. On his way to deliver the embryos to the island's docks, Nedry becomes lost, crashes his Jeep, and is killed by a Dilophosaurus.
Sattler, Victor, and Zecora assist the park's game warden, Robert Muldoon, in a search for survivors, but only find Malcolm and the others before the Tyrannosaurus returns and chases them in one of the vehicles, but ultimately fails to catch them. Unable to decipher Nedry's code to reactivate the security system, Hammond and the park's chief engineer Ray Arnold opt to reboot the park's computer and electrical network. The group shuts down the park's grid and retreats to an emergency bunker, while Arnold heads to a maintenance shed to complete the process of rebooting the system. When he fails to return, Sattler and Muldoon head to the shed themselves. They discover the shutdown has disabled the remaining fences and released the velociraptors; Muldoon distracts the raptors while Sattler turns the power back on, discovering the severed arm of Arnold afterwards. Soon after, the raptors ambush and kill Muldoon.
Alone in the park, Grant, Tim, Lex, Stephen, the CMC, Spike, Mako, Willy, The Miner Trains, and Shai-Shay discover broken shells of dinosaur eggs. Grant concludes that the dinosaurs have been breeding, which occurred because they have the genetic coding of frog DNA - West African bullfrogs can change their gender in a single-sex environment, which the dinosaurs were able to do as well. On the way back to the visitor center the trio encounter a herd of Gallimimus when suddenly the Tyrannosaurus appears out of the jungle and kills one. Grant, Tim, Lex, Stephen, the CMC, Spike, Mako, Willy, The Miner Trains and Shai-Shay reach the visitor cener. Grant leaves them behind as he goes searching for the others. After finding the bunker, Grant and Sattler, Thomas, Twilight, and the others head back to the visitor center, where the kids, and everyone else are being attacked by two velociraptors. They head to the control room and Lex restores full power, which allows the group to call for rescue. While trying to leave, Grant's group is cornered by the raptors but escapes when the Tyrannosaurus suddenly appears and kills both raptors. Hammond arrives driving a jeep carrying Malcolm, and the entire group flees together. Before they board a helicopter to leave the island, Grant says he will not endorse the park, a choice with which Hammond concurs.
- 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.
- The 3D release of Jurassic Park, Thomas & Friends: King of the Railway, and My Little Pony: Equestria Girls are all released in 2013.
- The storyline continues in Thomas and Twilight Sparkle visit The Lost World: Jurassic Park