A new Sodor Search and Rescue Center is being built for Harold, Rocky and Captain, a new lifeboat. Jobi wood is needed in order to build it, delivered from Hiro's homeland. All the engines want to help deliver the Jobi wood. Meanwhile, Diesel feels insulted after Thomas teased him for not being a steam engine. Diesel tries to prove his point by taking the Jobi wood himself, resulting in a chase between him and Thomas, and all the Jobi wood being lost in the sea after Diesel almost falls off an unfinished bridge. Thomas is rewarded with collecting new wood after rescuing Diesel from the bridge. Being told there is no room on the boat, Thomas asks to be carried on a raft behind the boat. However, along the way, the chain to the raft snaps and, after falling asleep, Thomas wakes up only to find himself landing on a nearby island, Misty Island.
Thomas explores the island and soon finds it to be inhabited by the "Logging Locos", consisting of Ferdinand and two small twins, Bash and Dash, who were sent to the island after causing trouble on the mainland. As Thomas continues exploring the island, meanwhile, back on Sodor, Sir Topham Hatt receives a call telling him Thomas is missing, prompting him, Harold and Captain send out a search party to find him.
After seeing the entire island (and traversing a shaky bridge known as the Shake-Shake Bridge), Thomas discovers a logging station which the Logging Locos are traversing around. He decides he wants to go back to Sodor and uses the Misty Island Tunnel, a tunnel that connects Misty Island to Sodor. However, as they are nearly halfway through the tunnel, the tunnel caves in on both sides causing them to get stuck. At the same time, the Logging Locos run out of oil. Thomas finds a hole in the ceiling of the cave which gives him an idea: he can puff smoke out through the hole and alert his friends of his location. The smoke soon alerts the rest of the gang of Thomas's location, convincing Percy and Whiff to go into the tunnel. Percy alerts Thomas of his presence, convincing Thomas he should break through the caved-in rocks himself. However, Whiff sternly corrects Thomas, saying he knows the tunnel more than he does. Thomas is soon convinced, allowing Percy and Whiff to break through. The three then haul the Logging Locos out of the tunnel and take them to be fixed up. However, Sir Topham Hatt, Edward, James and Gordon have all sailed to Misty Island in order to find Thomas, so Thomas rushes back to Misty Island and finds them just in time. Once he does, the Logging Locos are all welcomed to Sodor and there is a big celebration for the opening of the Sodor Search and Rescue Center.
In a post-credits scene, Diesel 10 from above the center watches down on the engines remarking they will laugh on the other side on their boilers soon.
Martin Sherman as Thomas and Percy
William Hope as Bash, Whiff, Rocky, Edward, Toby and Docks Manager
Kerry Shale as Dash, Harold, Gordon, James, Henry, Kevin and Sir Topham Hatt
Jules de Jongh as Emily
Glenn Wrage as Ferdinand and Cranky
David Bedella as Victor
Keith Wickham as Salty and Captain
Matt Wilkinson as Diesel 10
Togo Igawa as Hiro
Michael Brandon as the Narrator and Diesel
Ben Small as Thomas, Ferdinand, and Toby
Matt Wilkinson as Bash, Victor, Rocky, Cranky, Kevin, Docks Manager and Diesel 10
Keith Wickham as Dash, Harold, Whiff, Salty, Captain, Percy, James, Gordon, Henry, Edward and The Fat Controller