The movie opens to see an 58 year old man named Salior John where he is following a map to a magical book. He finds the book on the Island of Sodor and quickly snatches it from a cavern and quickly disappears just as Thomas the Tank Engine passes by. He quickly He returns to his ship where he reads the story to some Rats on board. The story is about Thomas, his friends and the Island of Sodor. It is a busy day on Sodor and Thomas is delivering some Bananas to the Zoo for the Monkeys until Devious Diesel bumps into his trucks and sends the Bananas up into the air and land on Thomas. Thomas gets so cross he and Diesel begin to have a fight until suddenly like magic the Island of Sodor turns into a post apocalypse and evryone thinks diesel and the other diesel engines are responsible but only Thomas believes that they're innocent so he comes to Diesel's rescue and his crew attach balloons to his and Diesel's buffers and they float away into the sky. The angry mob chases after them but manage to get away. After this the engines and people on Sodor go crazy.
Back in the real world, John finishes reading the story to the Rats and says that it ends with Sodor falling into despair and chaos. The Rats however, think otherwise and complain that the story shouldn't end that way. One of the Rats rips out the ending page and it lands into a secret portal to Sodor. Back in Sodor, the Island is still in chaos and the citizens & engines have gone psychotic.
Back in the air, Thomas and Diesel decide to work together to solve the crisis, Diesel is reluctant at first but eventually agress. They try to go and recruit the Steam Team only to find they've gone nuts so they escape. Especially the Troublesome Trucks became insane and part of a rebellion. Thomas & Diesel go to an abandoned railway from Sodor and they decide to camp outside and find a way to find the person responsible. Meanwhile Thomas' Driver Frank & Fire stoker Bob convince Diesel's driver Dave to help him and their engines together. Dave is hesitant at first believing Steamies & Diesels don't work together but eventually agrees. The next Morning Dave comes up with an idea which is: Go back in time and find the person responsible.
The first thing they need to do is find a generator to they secretly go the the Dieselworks (Which is guarded by Den & Dart and their drivers). Pretty soon Frank throws a dummy to Den & Dart and their drivers start beating it up, allowing Thomas & DIesel to sneak past the 2 diesels. They search in the works for a Generator, they have no luck seeing one until Dave finds one in the sheds. Diesel & Thomas then leave the Dieselworks with the Generator. Later at an abandoned Scrapyard, Dave, Bob and Frank all work together by finding spare parts and they succeed. The 3 crew go back into the wrong timeand find Christopher Awdry and seventuallyteal the wrong book (How to Turn Trains into Scrap) and return back to present. Meanwhile, Sailor John stops his Rail Boat to a local Train Station in Orlando FL. He scares all the Rats away with a bowl of Rat Poison.
Thomas & Diesel return to Tidmouth but instead find the book How to Turn Train into Scrap. Bubbles the Clown steals the time machine and brings back an actual Bigfoot Monster. Diesel blames Thomas for everything which causes Thomas to have a break down by crashing trucks into tankers. Thomas then stops and realizes what has become of everyone and they're let it happen. The people & engines realize that Thomas is right and set out to find the person responsible for turning Sodor into a post apocalypse.
After a long Journey, Thomas manages to track the sent of Sailor John when he first stoled book. He soon finds that it leads to a magic portal soon the minor characters leave except for The Steam Team & Diesel so they have to keep on going but they don't know if they come back alive. Just then a Wizard named Gearroid helps Thomas & Friends out by showing them what's on the other side and they find New York. All of the engines then go through the Portal and Thomas thanks Gearroid for helping them, Gearroid then bids them farewell and disappears magically.
The gang finally finds Sailor John telling people the story of how Sodor became an apocalypse state. The steam team encounters him and demand to know what's going on. John explains to them that he used a magic book to obtain the cause of Sodor into a post apocalypse. With Thomas and friends confused, John takes the magic book and writes "The brave and handsome Sailor John banished are poor heroes to become stranded on Death Island." With the Steam Team stranded on Death Island, it seems as if there is no hope until Driver Frank has an idea! He gets the paper that was ripped by the Rats and quickly rewrites the story.
As they return it is revealed that Frank gave the Steam Team super powers — The Jet Engine (Thomas), Super Strong Engine (Edward), Flying Kipper (Henry), The Bullet Express (Gordon), Super Spotless (James), Mail Train (Percy), Scrap Tram (Toby) Super Great Western (Duck), Amazing Scottish Twins (Donald & Douglas), Super Coolness (Oliver) and Emerald (Emily). They return & encounter John who drives off in his Sail Boat on Rails. During the battle the book is destroyed and John picks the team members off one by one to prevent them from retrieving the last page to return home. All hope is lost but then Diesel who'd been left on Death Island because a transformers diesel engine like hero named Wiesel and comes to help them.
He lifts the Track inspection Sailboat and places John onto the ground and tries to escape but Wiesel catches him. John finally surrenders and gives him the ripped off page. John tries to convince him to join him but Wiesel refuses saying he's already part of a time and sends him to the Moon. The Steam Team then return back to Sodor and fix the mess just before Sir Topham Hatt returns. On the moon Sailor John finds the Rat tribe already there and they ask if they can sing their favourite Thomas song Thomas We Love You, John agress and they all sing. Just as they're about to finish Neil Patrick Harris appears in a time machine and and argues with a rat that he doesn't like the song and the 2 engage in a rap battle. With the battle finished Neil allows them to finish the song, ending the movie
- John Hasler as Thomas/The Jet Engine
- Kerry Shale as Diesel/Wiesel
- Teresa Gallagher as Emily/Emerald
- Keith Wickham as Percy/Mail Train
- Hugh Laurie as Henry/The Flying Kipper
- Ringo Starr as Gordon/The Bullet Express
- Rowan Atkinson as Edward/Super Strong Engine
- Rob Rackstraw as James/Super Spotless
- Jim Broadbent as Toby/Scrap Tram
- Steven Kynman as Duck/Super Great Western
- Joe Mills as Oliver/Super Coolness
- The Umbilical Brothers as Donald & Douglas/Amazing Scottish Twins
- Nick Offerman as Sailor John
- Ian McKellen as Gearroid the Wizard
- Alan Marriott, Tom Fahn, Paul F. Thompkins, Hank Azaria, Paul Rugg, Rupert Degas, Lewis Macleod, Katt Williams, Billy Dee Williams, Vicki Eibner, Vincent Marzello and Jenny Slate as Rats
- Jon Lovitz as Wallace the Rat
- Dannel Henney as Driver Frank
- Lewis Black as Driver Dave
- Jason Sudeikis as Fireman Bob