Sir Topham Hatt, normally in charge of the railways on Sodor, is on holiday and has left Mr. Conductor in charge. Meanwhile, Thomas and Gordon encounter an evil diesel locomotive, Diesel 10, stating that he has unfinished business on Sodor.
Mr. Conductor has problems of his own. The mysterious gold dust that allows him to magically transport from place to place is running out, and without it there will be no way for anyone to travel from Shining Time to Sodor or back again. There is a lost engine that is able to travel between Sodor and Muffle Mountain using the Magic Railroad, but nobody knows where she is.
Burnett Stone, an elderly man, lives on Muffle Mountain, near Shining Time Station, in which Stacy Jones was the manager. Unknown to everyone, he is the guardian of the lost engine, whose name is Lady. The engine crashed after an earlier encounter with Diesel 10, and ever since then Burnett has been trying to repair Lady. But though he seems to have gotten the little engine restored mechanically, so far he has been unable to make her steam.
Percy and Thomas find out that there is a secret railway and there are magic buffers that lead to it. However, Diesel 10 overhears them. Toby the Tram Engine follows D-10 and hears him telling his diesel locomotive henchmen Splatter and Dodge of his plans to destroy the steam locomotives. Diesel 10 thinks that this horrid act seems possible mainly because Mr. Conductor's whistle contains gold dust inside which he uses to travel is running out, and he is therefore becoming too weak to stop Diesel 10. Wanting to warn his friends of Diesel's plans, Toby rings his bell, distracting them.
Burnett's granddaughter Lily visits him, and meets C. Junior, Mr. Conductor's good-natured but lazy cousin, who takes her to Sodor and introduces her to the talking engines who live there, including Thomas. Later, Thomas is assigned to transport Lily back to Burnett on Muffle Mountain after inadvertently discovered the entrance of the long-abandoned Magic Railroad by an old grotto. He takes his lost truck of special Island-of-Sodor coal and arrives on the other end of the Magic Railway, located at the edge of a high cliff near the top of Muffle Mountain. Lily goes to her grandfather's house, leaving Thomas stranded on the mountain. However, the ground gives way and Thomas uncouples himself from the coal-truck, falling off the cliff to the bottom of the mountain where he re-enters the Magic Railroad through another portal there.
Lily reunites with Burnett at his workshop, where he shows her Lady and explains his problem getting the engine to steam. Using the Sodor coal truck, the engine eventually comes to life. Lily and Burnett take Lady along the Magic Railroad, regenerating itself in the process. Lily comments that Burnett had never forgotten about Magic. The travelers reunite with Thomas and find their way back to Sodor, where Diesel 10 finds them and goes after them. He is foiled by a damaged viaduct which collapses beneath him, sending him falling into the ravine below, where he lands in a barge filled with sludge and is carried away.
Thomas, Lady, Burnett and Lily meet Mr. Conductor and C-Junior. They use the water from a wishing well and shavings from the rails of the Magic Railroad to make more gold dust, and the Island of Sodor and Shining Time Station are saved. C-Junior, encouraged by his success in being able to help out, offers to take a job on Sodor, and Mr. Conductor presents him with his conductor's cap and a spare uniform so that C-Junior can now assume Mr. Conductor's role on Sodor, while Mr. Conductor says that he will now travel back to serve at Shining Time Station. In the end Thomas is happily going home to Tidmouth sheds to tell the engines about his encounter with the lost engine Lady.
