Dino Clopman, Thomas and the Magic Railroad is a spin-off film created by Dinoco95. It's unknown if it will be shown on YouTube.
The film begins with Mr. Conductor introducing Thomas and Sodor.
Gordon complains to Thomas, who is late. The DinoAdventure Squad are on Sodor and have agreed to help out. Thomas retorts that Gordon is being bossy and says that he has to find Mr. Conductor, who is looking after the North Western Railway while Sir Topham Hatt is taking a holiday. Gordon claims Mr. Conductor is not needed, but changes his mind after Diesel 10 speeds by. Dino and his friends learn that a changeling has joined forces with Diesel 10, as well as a new enemy named Verminious Snaptrap.
Thomas, Dino and the others are later talking to James at Tidmouth Sheds when Diesel 10, the changeling and Snaptrap show up and voice their plan to destroy a lost engine and thus the remaining steam engines. James is confused, but Thomas is worried and goes to find Mr. Conductor.
After seeing Billy Twofeathers' map and noticing some strange lines on it, Patch heads off to Muffle Mountain to see Burnett Stone.
There is something on Muffle Mountain, a secret that Burnett only shared with his childhood friend and future wife Tasha: he promised he would drive an engine and take her with him. When Patch sees the engine, Burnett reveals the engine's past - her name is Lady, and she has been sealed inside Muffle Mountain since Diesel 10 nearly destroyed her long ago. Burnett has fixed her up, but still needs coal.
Diesel 10 tells his cronies Splatter and Dodge of his plan. The changeling says that he and his brainwashed Rattleoid will get rid of Dino and his friends to keep them from foiling Chrysalis' conquest of Earth, as well as Equestria and Vestroia. The two bumbling diesels report that Mr. Conductor is coming to Sodor, so Diesel 10 decides to destroy him too.
Mr. Conductor prepares to leave Shining Time, and he meets T.U.F.F. agents Dudley Puppy and Kitty Katswell, who have been assigned by their chief to go to the human world and stop Snaptrap. Despite difficulty with his gold dust, he transports them to Sodor and soon meets Thomas on Sodor. Thomas reports on Diesel 10; Mr. Conductor decides to use his gold dust to keep Diesel 10 in order.
Burnett looks at a painting of Lady and starts to have doubts in his belief of magic due to his failure to guard her. Meanwhile, far away, Burnett's granddaughter Lily prepares to visit him.
Thomas, James and Gordon begin arguing about who should have taken Mr. Conductor, unaware Splatter and Dodge are spying on them, along with the changeling, Rattleoid, and Snaptrap's henchmen. The DinoAdventure Squad trade information with Dudley and Kitty. Splatter and Dodge tease Thomas, until Harold flies by, spreading dust over all of them.
At Knapford, Mr. Conductor reads the note Sir Topham Hatt left him. After trying on his top hat (and returning it after he notices the portrait of the Controller appears angry) he receives a phone call from Sir Topham Hatt and receives his instructions.
That night, Diesel 10, the changeling, his Rattleoid, and Snaptrap creep up and demolish the side of the Tidmouth Sheds with their powerful claw, fangs, and ray gun, respectivly. Mr. Conductor reprimands Diesel 10, but then he discovers that he has run out of gold dust. Rattleoid grabs Dino and threatens to harm him if the others don't tell the villians about the lost engine. Diesel 10, delighted, tries to convince Mr. Conductor of the lost engine's whereabouts, but Mr. Conductor frightens Diesel 10 away with a bag of sugar. Mr. Conductor voices his concern about his gold dust, but tells the engines and others to go back to sleep.
Mr. Conductor later has a nightmare of Shining Time in ruins, and realises that his universe is in danger and that he needs more gold dust.
The next morning, Mutt goes to Lily's hometown with Billy, as he knows that Lily can help Mr. Conductor, but only if she meets someone special at Shining Time first. To reach that end, he directs her onto the wrong train.
Mr. Conductor goes to the windmill in search of more gold dust, along with MattLin and CatDog, but gets lost. Meanwhile, the engines, Dino, and others gather for a meeting. Bertie passes by and tells them to smile, but all have their individual concerns. Thomas, the DinoAdventure Squad and agents head off to look for Mr. Conductor.
Mr. Conductor tries a carrot and a stick of celery to make him think properly, and has the idea his beach-loving cousin Junior, who has used up most of his gold dust too. He tells Junior to go to Shining Time and get his emergency whistle, then go to Sodor, and warns him not to talk to anyone about the buffers. Before he can say anything else, the line goes dead.
Lily arrives at Shining Time and Mutt barks at her to get off the train. Lily finds the station empty and meets Junior. After a talk, Lily picks up the gold dust Junior leaves behind. At Sodor, Mr. Conductor is sleeping by a bush when he has another nightmare, and wakes up hearing Thomas calling his name. Mr. Conductor tries to reply, but Thomas cannot hear him.
Lily meets Stacy, who takes her to Burnett. That night, Burnett and Lily hear Lady's whistle coming from the mountains; Patch, who is outside with his horse, hears it too.
Thomas, Percy and the others talk about Mr. Conductor and conclude that he travels to Sodor on a magic railroad. Diesel 10, the changeling and Snaptrap overhear them and go to the scrapyards to tell Splatter and Dodge, Rattleoid, and henchmen their plan. Toby interrupts them by ringing his bell; Diesel 10, trying to catch him, causes the shed to crash down on all the villians.
Thomas, Dino and his pals find Henry with a bad cold and offer to get some Welsh coal to make him better, but while collecting them, fail to notice the sixth truck bouncing away into some magic buffers. Bertie passes and greets Thomas and his five trucks; Thomas is confused.
Thomas tells Percy about the missing truck, and they realize that the buffers where the truck disappeared are the buffers leading to the Magic Railroad. Thomas tells Percy to guard the buffers while he goes to find Mr. Conductor. Hamtaro says he'll help Percy.
Meanwhile, Mr. Conductor and the hybrids are wandering aimlessly when Diesel 10 appears. They are captured by Diesel 10's claw and are dangled over the viaduct. Diesel 10 reveals he knows about the buffers, and threatens to drop everyone if they doesn't reveal their whereabouts. Mr. Conductor cuts a tube to Diesel 10's claw, catapulting him and the others to the windmill. There, he sees the words "Stoke up the magic in the mountain and the Lady will smile, then watch the swirls that spin so well".
Lily is introduced to Patch, who offers her a horse ride to Shining Time. There she meets Junior again, who takes her to Sodor via the magic buffers. They meet Thomas and the others, who agree to help, and together they find Mr. Conductor at the windmill. Mr. Conductor tells Junior about his clue to the gold dust, and Lily is introduced to Mr. Conductor. Junior and Dudley then climb onto the sail, and are flung onto Diesel 10.
That night, Percy and Hamtaro find Splatter and Dodge and the other bad guys at the magic buffers and race to warn Thomas and Dino.
Mr. Conductor and Lily camp out with Thomas, Dino, his friends, and Kitty. After a conversation, they realise that Burnett may hold the key to the clue of the gold dust.
Burnett reveals to Patch that Lady is magic and they realise that the railroad is vanishing.
Thomas and Percy decide they must get Lily back to Muffle Mountain before Diesel 10 and the other villians destroy the magic railroad, and Thomas, Lily and the DinoAdventure Squad set off. While journeying through the magic railroad, they discover the missing truck. Lily, realising the connection between the truck and the clue, asks Thomas to collect the truck. They soon arrive on Muffle Mountain. Lily, Dino and the others leave to find Burnett, but a gust of wind blows Thomas down the hill and back into the magic railroad through a mysterious portal at the bottom.
Lily and the Squad find Patch, who takes them to Burnett's workshop. Lily figures out only Welsh coal can make Lady steam, so she sends Patch to collect the coal from the truck.
Diesel 10, with Junior and Dudley still on his back, races into the Smelters where he encounters James. Junior tries to whistle the three of them out, only to discover that he too, is out of gold dust. Diesel 10, along with Rattleoid, try to force the three into a melting pit. Junior makes a sacrifice, and uses the last bit of gold dust to teleport himself, Dudley, and James away. They arrive near the buffers, where Mr. Conductor is there waiting. Mr. Conductor and Junior, both out of gold dust, refuse to give up hope.
By now Burnett Stone has finally got Lady to steam, and along with Lily, Patch, Mutt, and the DinoAdventure Squad, they set off into the magic railroad. The magic railroad, receiving energy from Lady, comes back to life, while Lady's face appears. The team encounter Thomas before appearing on Sodor, where they reunite with the two conductors and agents.
Diesel 10, the changeling, Rattleoid, and Snaptrap start to give chase, but Splatter and Dodge, fed up with Diesel 10's ways, abandon him. Thomas, Dino and the others offer to help Lady, with Burnett driving Lady. Mr. Conductor warns them about the collapsing viaduct. Just as the engines run away, the conductors realize that Lady is part of the clue to the gold dust.
The chase finally approaches the viaduct. As Lady and Burnett pass, a gap appears on the viaduct. Thomas manages to jump through the gap, but Diesel 10 cannot stop in time. Rattleoid is hit by a burst of energy from Leonidas, breaking the brainwashing spell, and Snaptrap's jet runs out of fuel. They all fall off into a sludge barge (Diesel 10 looks on the bright side by saying it is a nice time of the year for a cruise). The changling returns to Equestria and Snaptrap plots his revenge against T.U.F.F.
Thomas, Lady, Burnett and the others return, where they and the rest of the team work out on the answer to the riddle. Lily mixes water from the well with golden shavings from the magic railroad, and tosses them into the air, where they form into gold dust. The conductors, delighted, re-supply their whistles, while Thomas thanks Lady.
Patch and Mutt go to look around, while Junior gives Lily some gold dust. Junior tells Mr. Conductor that he wants to work now, so Mr. Conductor gives him his hat and sends him to a railroad with "palm trees and sunny spells". After Junior leaves, Sir Topham Hatt calls and says that he is on his way back, so Mr. Conductor sets off to welcome him. Lily offers her gold dust to Burnett, who sprinkles it on her bluebird toy and whispers that they will "always remember their Shining Time together". Dudley and Kitty's boss arrives and congratulates them.
With Lady and the Magic Railroad back to life, Shining Time is restored to its former glory. Thomas happily puffs into the sunset, the DinoAdventure Squad leave on a new adventure, and the end credits roll.