This railroad procedural drama, based on the Railway Series by the Rev. W. Awdry, follows the locomotives of the Principality of Equestria and their crew, as they defend themselves against an assault from big monsters with magical powers.
Rheneas takes a full passenger train back to Canterlot on only one spring during a thunderstorm, and has to go for an overhaul. Edward the Blue Engine has to be sent for repairs after rescuing James the Red Engine, during which time he meets Skarloey, who is also retired from service due to his age. Meanwhile, new engines Sir Handel and Peter Sam are fetched over by new controller Jay Halstead to help with the workload.
Sir Handel's first day on the job proves to go better than expected for the young "hakuna matata" engine. He takes a passenger train to Canterlot, where he meets Gordon the Big Engine. But the next day, Controller Halstead and chief engineer Reno Raines discover that Sir Handel is in a deep sleep...
Due to Sir Handel's boiler being cleaned up of the mysterious substance, Peter Sam is tasked to relieve Sir Handel's duties. Trouble ensues however, when due to negligence on Controller Halstead's part, Peter Sam accidentally leaves Pinkie Pie behind at Horseshoe Bay Sands station...
Peter Sam is sent for an overhaul. Sir Handel once again runs the line, but has to check suddenly at a fallen branch on the line, causing him to burst his safety valve. Without another engine available, Skarloey daringly decides to come out of retirement and take over. The Four Ponies of Hakuna Matata are introduced...
A new engine, Duncan, comes from Scotland to help Sir Handel run the line. Peter Sam, Skarloey, and Rheneas all return from their overhauls. The evil witch Morgana Pendragon attempts to inflitrate her way into Equestria using her expertise of disguise...
Sir Handel does not believe in mountain railways, until he meets a purple mountain engine named Culdee - who so happens to be Duncan's old friend from back in their days on the Appalachian Mountain Railway. Meanwhile, Douglas the Scottish Twin Engine takes a goods train to New York City, where he rescues Oliver the Great Western Engine and his brakevan Toad from a scrapping yard - which turns out to be owned by Morgana Pendragon...
Culdee returns to his home railway, the Yakyakistan Mountain Railway, where he rejoins his colleagues Godred and Patrick, and their controller Hitch Trailblazer. Godred mentions that there had been a mysterious female passenger loitering around at Griffonstone Station. Meanwhile, important evidence in Canterlot Castle goes missing, and Controller Applejack holds Reno and Controller Halstead responsible...
Godred has a magical showdown with Morgana. Princess Luna rescues Duke the Wise Old Engine, who had been trapped under the rubble for many years. Duke is assigned to help run the narrow-gauge line.
The narrow-gauge engines discuss how they are going to deal with Morgana and her magic. Reno proposes to Halstead. Skarloey learns magic from Snails the unicorn.
Ivo Hugh is the newest engine to join the narrow-gauge fleet, and also the strongest and only side-tank of his colleagues. However, his weakness is his chronic lethargy, which proves to be a problem for Controller Halstead, who is forced to get Duncan to relieve Ivo Hugh's duties.
Skarloey and Morgana duel each other magically at Dolgoch Falls, by transmogrifying themselves into various life forms. The conditions are simple: No disappearing, no "fantastical creatures such as green dragons", and no cheating. See who starts off with a win...
Taking advantage of the precarious situation in Equestria, Lex Luthor infiltrates furtively and tries to hold a conference in Shangri-La Hotel in Manehatten purportedly under the name of an "international security conference". Against their own wills, the five big engines - Gordon, Henry, James, Donald, and Douglas - are tasked to literally gatecrash the hotel to force the intruders out...