The Lost World: Chuggington is the first special of Chuggington: Meet Thomas, Trainees!. It follows the same plot of Jurassic Park: The Lost World, but with Chuggington characters and Thomas in it.
Four years after the incident at Chuggington Jurrasic Park, Vee has lost control of Chuggington to her nephew Howard Jensen. Dunbar violated his non-disclosure agreement and went public about the events, but few believed him and threats of legal action prevented him from producing any evidence, leaving his academic reputation destroyed. One day, Vee summons Dunbar to his shed and tells him about "Site B", located on Isla Sorna, where the dinosaurs were actually engineered, before being sent to Isla Nublar when mature. The island was abandoned after a hurricane wiped out most of the facilities, and the creatures were left there to live wild. Vee asks Thomas and the trainees to help her stop Jensen from using Site B to bail out the bankrupt Chuggington, and to help him convince environmentalists to leave the island as a nature reserve. Thomas and the trainees initially refuse, but agree to go after learning that Hodge's girlfriend, paleontologist Zephie, is already there.
Thomas, the trainees and Dunbar are joined by Irving, an engine who recycled the group's custom vehicles, and Harrison, documentary producer, environmentalist and speed record breaking engine. Shortly after arriving on the island, they encounter a Stegosaurus herd and meet Zephie. When they return to camp, they find Fixer, the trainees, Thomas and Hodge's old friend, has stowed away. Thomas tries to contact the boat to take them home, but they are interrupted by the arrival of an InGen team sent by and joined by Jensen. The rival team quickly captures samples of several species, including Parasaurolophus, Stegosaurus, Gallimimus, Pachycephalosaurus, Triceratops and a swarm of Compsognathus. That night, Hodge and Zephie sneak into the Chuggington camp to free the dinosaurs and cut the fuel lines on the vehicles. The freed dinosaurs cause a huge commotion as they escape, compounded by the exploding vehicles. Chatsworth, the leader of the Chuggington team, admonishes his second-in-command, Emery, for the lack of security.
Chatsworth wishes to capture an adult male Tyrannosaurus, and creates a trap by breaking the leg of a baby T. Rex so that its cries might lure its parents. When he returns to the camp, Thomas frees the baby, taking it back to their trailer so Danny, Riko, Echo and Austin can set its broken leg. The adult Tyrannosaurs come searching for their child and, after retrieving it, throws one half of the hinged trailer over a cliff with Thomas, Koko, Wilson, Brewster, Hodge, RJ, Fixer, the boys, and Zephie inside. Irving throws down a rope and tries to pull the trailer back up using one of the SUVs, but his SUV gets ripped up by the Tyrannosaurs and is torn in half and the SUV is eaten (but not Irving). The trailer falls off the cliff, but its occupants survive by holding on to the rope, only to be rescued by Chatsworth and the Chuggington team. With all of the communications equipment destroyed in the attacks, both groups team up to reach the old Chuggington compound's radio station, right through a Velociraptor nesting site. During the walk to the station Emery is killed by a pack of Compsognathus.
At night, the male Tyrannosaurus comes across the group's camp and pokes his head into Zephie and Fixer's tent, sniffing Sarah's jacket covered with blood from the baby's leg. One of the Chuggington team workers notices this and screams, waking up the rest of the group as they all begin to run, with the female Tyrannosaurus in pursuit. After initially failing to kill the male Tyrannosaurus (mainly because the boys stole the bullets from his gun), Chatsworth uses a tranquilizer gun to knock the dinosaur out. After fleeing from the female Tyrannosaur, the Chuggington team pass through a field of tall grass and are picked off one-by-one by Velociraptors. Thomas, the trainees, Dunbar, Harrison, Irving, Zephie and the boys pass through the field unharmed and Irving reaches the compound, but the others are attacked by three raptors and go into hiding. After a fight with the raptors, Thomas, Zephie, and Fixer run towards a building where they reunite with the boys and contact a rescue helicopter. As they fly away, they see that Chatsworth has caged the male Tyrannosaur and Jensen preparing to ship it and the baby back to the mainland. However, Chatsworth is depressed over Ajay's death (from the raptors) and resigns his post in Chuggington, declaring to Jensen "I think I've spent enough time in the company of death." He then walks away towards a helicopter.
When the ship carrying the dinosaur arrives in San Diego, it crashes into the dock. A boarding party finds out the entire crew is dead. While searching for survivors, a guard opens the cargo hold and inadvertently releases the Tyrannosaur, which escapes into the city. Thomas, the trainees, Hodge, Dunbar, Harrison, and Zephie learn that the Tyrannosaur stopped breathing due to a tranquilizer overdose, it was given amphetamines to bring it around, but not knowing the proper dosage, they administered too much and the dinosaur is out of control. Realizing that the Tyrannosaur will likely come for its infant, Thomas and Hodge rush to the Jurassic Park arena to get the baby T. rex, which had been brought in separately by plane, and during this time, the T. rex is wreaking havoc in San Diego, having eaten a fleeing civilian and a dog. They lure the adult with the baby and run back to the boat. Jensen tries to intervene, but is trapped in the cargo hold and devoured by the baby. Thomas, the trainees, Dunbar and Zephie manage to tranquilize the adult before it can escape again, and seal it in the hold.
By morning, as Hodge and Zephie fall asleep on the turntable in their living room, Fixer watches television reports of the cargo ship on its way back to Site B, surrounded by a convoy of naval vessels. The program breaks away to an interview of restored Chuggington Chairwoman Vee, who explains that the island will now be left alone as a natural reserve so the dinosaurs can live free of human interference. She offers a quote by Thomas, "Life will find a way." The scene cuts to Site B, where the family of Tyrannosaurs is shown reunited in the wild, alongside a herd of Stegosaurus migrating and a flock of Pteranodons flying overhead.