A bright portal appears on the top of a green hill and Terra walks out of it in his armor. The metal covering his body disappears and he looks around to investigate the environment. He then hears the sounds of train whistles echoing far away. Terra looks down the hill to see a lot of trains in different colors moving along some tracks in the distance. He notices that all of them have faces and thinks "This is nothing like any of the other worlds. It's unique, but what forces of darkness would want to take over this place?"

Terra hears a whistle blowing and turns around to see a small blue tank engine smiling at him. "Hello there, sir! Are you lost?" the train asks him. Terra looks at the engine in surprise and quietly says "I must be dreaming. These things can talk too." The blue train looks at him in confusion saying "What was that? I didn't hear you." Terra calms down and replies "Never mind. It's nothing. My name is Terra. Have you ever heard of a man named Xehanort or seen any dark creatures running around?" The tank engine responds "I don't believe that I have. I'm sorry. By the way, my name is Thomas! I'm looking for someone too. If we find him, then maybe he will have a proper answer for you!" Terra nods his head and says "Alright then. Lead the way." Thomas moves forward and Terra follows him on a path that is right next to the railroad.

After a few minutes, Thomas blows his whistle and shouts "There's Mr. Conductor! I knew we would find him!" Terra and the blue train stop to see a man in a blue conductor outfit with a whistle on his necklace. The two men greet each other and shake hands. Thomas looks at Mr. Conductor with a worried expression and says "Our big bully, Diesel, is back again, Mr. Conductor!" The conductor responds "Sir Tophom Hat warned me about that in a message he sent me. We need to head over to the train station and see if he's still there." Both Mr. Conductor and Terra jump onto the back of the train. Thomas blows his whistle and proceeds to drive forward.

They make it to the train station and Mr. Conductor jumps out of Thomas saying "I'll be in Sir Tophom Hat's office looking for him. Wait here and then I'll give you further instructions." He then walks inside of the office area of the train station. Terra jumps out of the blue train and views the empty station with a calm face. Thomas looks over at Terra and says "With Sir Topham Hat on vacation, things will be a little different around here for a few days. I'm excited, but also nervous at the same time." Terra walks over to Thomas and asks "So who is this 'Sir Topham Hat' guy?" The blue engine replies "Oh he is the one who runs the railways here on the Island of Sodor. However, Diesel 10 is back and he has caused some trouble here on the island in the past." Terra gives Thomas a look of confidence and says, "I'm sure everything will be all right."

Mr. Conductor walks out of the office saying "Thomas! Terra! We're ready to start the day." Thomas gives Mr. Conductor a big smile and says "Oh boy! What's the plan, Mr. Conductor?" The conductor looks at both of them explaining "Thomas and I will be taking care of some business around the island. Terra, can you help me with a little side project?" The keyblade wielder walks up next to him and says "I'm not going anywhere soon. What do you need me to do?" Mr. Conductor responds "Can you please look around for a tall windmill? I believe it will help us find clues to why magic is disappearing from this island. Without the magic, this world won't exist." Terra looks at the ground with a puzzling look and thinks to himself "So there is darkness in this world. Now I know why I was led here." He aims his head back up at the man in the blue uniform and says "Sure! I'll try my best." Mr. Conductor nods his head saying "Thank you, Terra. You're a very useful friend." He then jumps onto the back of Thomas and they drive out of the station. Terra runs through the station's entrance and goes to explore for the windmill.

Meanwhile near Shining Time Station, Ventus lands on the top of Muffle Mountain. He looks down at the large forest of trees below. He soon notices a man in a brown jacket walking into a secret cave. The young boy runs down the hill and follows the man. He peeks inside to see nothing but darkness. A bright light from a flashlight shines onto his face seconds later. Ven covers his eyes as he hears the voice of the man saying "Who are you and how did you find me here?" The boy lowers his arms and replies "If you turn off the light, then I'll introduce myself." The flashlight turns off and he sees the silhouette of the man a few feet away. He looks over at where the flashlight was and says, "My name is Ventus, but you can call me 'Ven' for short. I promise that I'm not here to hurt you." The man points at the wall behind the boy saying "See that switch over there? Flip it on." Ven walks over to where the man was pointing, notices the switch, and turns on the lights in the cave.

Ventus turns around to see a small purple train that stood lifeless next to some tools that are placed on a table. He walks over next to the man and says "I thought there would be something special in here. What is it?" The man walks up to the train saying "This engine's name is Lady and she is very important to me. Kind of like an old friend. By the way, my name is Burnett. So what can I help you with, Ven?" The young boy responds "I'm trying to look for some friends of mine. Their names are Terra and Aqua. Do you know them?" Burnett looks down at the ground with a sad look on his face and says "No. I'm sorry." He looks up and continues "However, there is a place near here called Shining Time Station. They could be there." Ventus nods his head and thanks Burnett for the advice. He then walks out of the cave and travels along a road down the mountain.

At Shining Time Station, Ventus notices that there is no one there. He walks inside of the station building and looks around to see if he could find anyone to help him. The boy sits down on a chair next to a painting of a train and looks down while letting out a sigh of sorrow. Suddenly, a little bright light appears in front of the painting and quickly vanishes to reveal a tiny man wearing a conductor outfit. The small person looks up at the boy with amazement and says in a Scottish accent "Hi there! Who are you?" Ventus responds "I'm Ventus. Call me 'Ven'. Who are you?" The little man bows forward saying "People call me 'Junior'. You seem worried. Did you miss your train?" The keyblade wielder looks at Junior with confusion and replies "No. I'm just looking for my friends. Do the names Terra or Aqua ring a bell to you?" Junior shakes his head saying "Nope, but they could be where I'm headed. The Island of Sodor! Want to come?" Ventus happily looks at the tiny man and says "Sure! I might have better chance of finding them there than here."

Junior holds a whistle near his mouth and looks at Ventus saying "Okay. Get ready! This is going to be a bumpy ride." He blows on the whistle and the two of them get sucked into the train painting. They then find themselves flying in a dark tunnel that looks to be abandoned and there is a rusty track below. Ventus looks over at Junior with surprise to notice he is now taller and almost the same height. He comments "You've gotten bigger!" Junior looks over at the boy and replies "Well that's what happens when I travel. I'm small in one place and tall in another." He looks forward, and continues speaking "This tunnel used to be so lively. It looks like the magic is truly fading away. Oh! Here come the buffers. Hold on!" At the end of the dark tunnel, there is a bright light and the two of them jump through it.

Junior and Ventus land on a green hill next to a railroad. They stand up and see a bunch of trains riding on some tracks in the distance. Junior looks over at Ven and says "We made it. This is definitely the Island of Sodor." Ventus continues to look at the view saying "Wow! So where do we go next?" Junior looks back at the view of the train tracks and says "Well, I need to find my cousin and you need to find your friends." He turns his head to look at the boy again, and continues "It was good to meet you, Ven. Good luck finding your friends. I'll see you around." He turns around and begins to walk away. After a few seconds, he stops and looks back at Ventus saying "By the way, look out for Diesel 10! He's a dangerous fellow." Right as the young boy turns his head to ask a question, Junior blows his whistle and disappears. Ven then looks over to see a road and walks down the path.

In another part of Sodor, Terra finds himself in front of the sheds where the trains rest at night. Thomas, James, Percy, Toby, and Gordon are talking about how Mr. Conductor may have lost his Gold Dust. Terra joins in their conversation saying "Don't worry. I'm sure that you'll find this magic again soon. You all need to have confidence." Toby looks over at Terra and responds "Well, if Diesel finds the Gold Dust and the lost engine that used to reside here on Sodor, I'm afraid that will destroy us all." Gordon shouts "What? Even an engine as big as me?" Toby looks over at Gordon and replies "Yes, Gordon, even you. It's the only source of light that keeps this island alive." Terra looks at all of the trains with confidence and says "Tell you what, I promise you that I'll help you find this 'Gold Dust' and keep the island safe for you while I'm here."

As Terra turns around to continue his quest, he sees a big Unversed that looks like a train. All of the engines back into their sheds with worried expressions on their faces and the doors close tightly. This leads into a battle between Terra and the monster. The Unversed is made up of three separate parts which are the steam engine (the front), the passenger car (the middle), and the caboose (the back). They are mostly connected together, but the three parts separate and attack all at once during the final part of the fight. When the battle ends, all of the engines come out and thank Terra for protecting them. The keyblade wielder nods his and runs off to continue looking for the windmill.

After running around for a bit, Terra finally comes across the windmill. He looks at it with a smile of relief and says to himself "Good. At least we know that the windmill is safe." Near the building, a dark portal appears and Vanitas walks out of it. The masked boy looks over at Terra saying "Take a look at this world. It's so pitiful and weak." Terra summons his keyblade and stands in fighting position shouting "You! The boy in the mask! What are you doing here?" Vanitas looks up at the windmill and replies "Why would you bother with such a stupid-looking world? This place doesn't need you." Terra looks at him in anger and responds "Stupid? You're the one who's acting stupid around here!" Vanitas summons his keyblade and says "Grow up, wimp." Now it's Terra's turn to fight Vanitas!

At the conclusion of their battle, Vanitas makes a dark portal appear next to him and says "You should be using your strength in other worlds that are in more danger." Terra looks up at him in confusion asking "More danger?" The masked boy walks into the portal and continues "Go out there and find out. You're wasting time here." When the portal is gone, Terra looks up at the sky and ponders "If there truly is more danger, then I need to get going. The windmill is here and in perfect shape. Forgive me, but I need to help others at this time." He puts on his armor, transforms his keyblade, and flies away.

Meanwhile in another area of Sodor, Ventus is walking on a bridge with a worried look on his face. In the distance he hears a grumpy voice shouting "Get out of my way!" The boy turns around to see a diesel engine with a claw attached on the top. The mechanical villain is charging at him. Ventus summons his keyblade and stands in a fighting position on the track that the diesel is driving on. The engine stops in front of him and shouts "Move or I'll run you over!" Ventus responds "Are you the one they call 'Diesel 10'?" It moves closer to him and replies "Yeah, but that's none of your business. Move it, kid!" Ven looks at him in anger and says "Not while I'm around. You're going to have to get past me first!" Diesel 10 looks at the keyblade wielder with an evil grin and replies "Oh! This will be fun!" This then leads into a fight between Ventus and Diesel 10. The engine will use his claw to pinch the warrior and a few Unversed appear to assist the villain as well.

When the battle concludes, Diesel 10 grabs the lower half of Ventus with his claw and lets out a little evil laugh. He moves his claw over the side of the bridge and says "I suppose you know where the buffers are. Tell the location now!" Ventus struggles to get out and replies "I don't know what you're talking about." Diesel 10 shouts "I'm gonna give you to the count of ten to answer me." As Diesel counts down, Ventus uses his keyblade to cut one of the cords near the claw. This causes the claw to launch upward and throw the boy into the air. Diesel 10 watches him fly away and lets out a little growl of anger.

After a couple of seconds, Ventus lands on a bush next to the windmill. The voice of a Scottish man shouts "Ven! It's good to see ya!" The boy looks up to see Junior running up to him. Ventus stands up and greets his friend. Junior turns around to look over at Mr. Conductor and says, "This is my cousin." Ven and Mr. Conductor shake hands as they greet each other. Junior looks at Ventus and asks, "So what are you doing here?" The keyblade wielder responds "Well I was looking for my friends, but then I came across Diesel 10. He grabbed me and threatened to drop me off the side of a bridge. I escaped from his claw and now I'm here with you guys." Mr. Conductor replies "It's good to see that you're alive." He then aims his body over at the windmill and continues "We were supposed to meet Terra here a while ago. I hope he's all right." Ven looks at the two of them with excitement and says "Terra? You know Terra? He's one of my best friends! Where did you last see him?" Mr. Conductor responds "I don't really remember. He could still be somewhere on the island." Ventus nods his head saying "Right! I'm going to look for him. Thank you." He then runs away with big a smile on his face.

The young keyblade wielder continues to look for his friends, but has no luck in the process. However, he does come across Thomas and the two of them greet each other. The blue engine asks, "Can you help me with a mystery that I'm trying to solve?" Ventus replies with a smile and says "Sure! What it is?" Thomas looks forward on the track he is on and responds "I need to look for some special buffers. I was told that they it will help me find a way to bring magic back into this world." The boy remembers that he flew out of some buffers with Junior and tells Thomas about it. They then move forward looking for it.

Thomas and Ventus soon find the buffers. The two of them agree to go in together. "Hop in!" shouts Thomas as he looks at the buffers with confidence. Ventus jumps into the back of the blue train and they begin to move forward. Both of them make it through the secret portal and look around the abandoned tunnel as the blue engine continues to slowly drive forward. In the distance, they see a coal truck sitting on another track. Thomas looks at it and says "What is a coal truck doing in here? Let's bring it with us. It could be really useful." They go onto the other track, hook up the coal truck to Thomas, and proceed to drive through the rest of the dark tunnel.

When Thomas and Ventus exit the tunnel, they find themselves on Muffle Mountain. Thomas looks around with a worried look asking, "Where are we?" Ventus replies "Muffle Mountain!" He jumps off of the train and runs away. Thomas looks over at him and shouts "Where are you going? Please don't leave me!" The keyblade wielder turns around and says "I'll be back, Thomas. I just need to see someone first while we're here!" He continues to run as he hears Thomas say "Please hurry! I'm feeling a little dizzy."

Meanwhile on the Island of Sodor, Aqua lands in an area that has factories and big sheds. She looks around and ponders "What is this place?" A few seconds later, she hears the sound of two people screaming in one of the buildings. The woman turns her head to look at the building saying, "What?" and runs over there to investigate. As she walks up to a large door in front of the shed, she notices that there is a large lock with a keyhole next to it. Aqua summons her keyblade and shoots a beam of light at it. The door slowly opens and the woman runs inside while making her weapon disappear.

When Aqua enters the building, she witnesses Junior and James being taunted by Diesel 10. The red train backs up into a broken buffer that is holding him from entering a hot furnace that is behind him. Aqua looks at the engines thinking "Are those things…alive?" Diesel 10 slowly moves closer to the two victims with more taunts, but Aqua stands in front of Diesel 10 shouting "Enough! Quit picking on these people!" The diesel looks at her with an evil smile and says "Well! What do we have here? Another brat for me to mess with?" Aqua summons her keyblade and stands in her fighting position saying "Alright! You asked for it!" This leads into a short fight between Diesel 10 and Aqua.

As the fight ends, Junior uses the last of his Gold Dust to teleport himself and James out of the building. Diesel 10 looks up at where the red train was in shock shouting "Huh? No!" He looks down at Aqua with anger shouting "You! Get out of my way!" She looks up at him with a little smile saying "Gladly!" She then runs over to the big shed door, presses a button, and causes the door to quickly block the exit. The woman stands in front of the door taking a breather as the voice of Diesel 10 shouts "Hey! Let me out of here!" Aqua looks over at some railroad tracks and ponders "I wonder if there is any other danger here?" She proceeds to run in the direction of the tracks with a look of determination.

On Muffle Mountain, Ventus finds Burnett Stone in the cave and says "Mister Stone! I need you to help me with something. I came back from the Island of Sodor and they said that they're looking for a lost engine. They could be talking about your train. The magic is slowly disappearing and they need you to help them. I have some coal from the island that could be useful for you." Burnett looks over at him with confidence and says "Ven, bring the coal here. It looks like Lady is ready to wake up." Ventus nods his head and runs back to where Thomas is.

At the top of the mountain, Vanitas appears behind Thomas and disconnects the blue engine from the coal truck with a strike from his keyblade. Thomas begins to move forward and proceeds to run down the mountain while letting out a worried scream. At the bottom of the hill, the train surprisingly goes through a secret entrance to the tunnel back to Sodor. Ventus runs over to see that Thomas is gone and notices that Vanitas is standing in front of the coal truck. He summons his leyblade and looks at the masked boy shouting "You! What have you done with Thomas?" Vanitas looks over at him and replies "That little engine is gone. Now to take care of this stupid coal truck." Ventus moves a little closer to him and stands in his fighting position shouting "You're going to have to get through me first!" This then leads into a fight between Ventus and Vanitas. After the battle, Vanitas jumps behind the coal truck and says "Stop wasting your time here. Go play your little games somewhere else." A dark portal appears over Vanitas and makes him disappear.

Ventus quickly brings some coal to Burnett and they start to fill Lady. The train begins to steam, and Burnett pulls on a wire to make the engine let out a little whistle sound. Ven jumps off of the machine and looks at the man with a grin. Burnett looks over at Ventus with a little smile and says "Thank you for everything, Ven. I'll make sure that the magic successfully returns to the island. Now go and find your friends." Ventus nods his head and waves to Burnett as the train moves forward into the little dark tunnel. The keyblade wielder then walks outside, puts on his armor, and flies away to explore some of the other worlds.

Back on the Island of Sodor, Aqua comes across Junior and Mr. Conductor. They greet each other and shake hands. Mr. Conductor asks "Aqua, have you seen a young boy, named Ven, around here by chance?" Aqua looks up at him with a surprised expression on her face saying "You know Ven? What was he doing here?" Junior responds "Well, he was helping us with this mystery that we're trying to solve, but it seems that he may not be coming back." Mr. Conductor continues "We're looking for the lost magic that helps this world stay alive. We'll all be destroyed if we don't find it soon. Will you help us solve the last of this mystery?" Aqua nods her head and says "Sure. Any friend of Ventus is a friend of mine. So what's the plan?" Junior replies "We're supposed to be looking for the lost engine, but we don't know where it is."

In the distance, Thomas runs up next to the three individuals and shouts "Hey, everyone! I found the lost engine!" Right behind Thomas is Lady with Burnett Stone riding in the back. Burnett looks around to notice that he is on the Island of Sodor and a little smile appears on his face. He jumps out and greets the three who are standing nearby. Junior walks up next to Lady with an excited look on his face and shouts "This is the lost engine? This is great! Now we can go back to Shining Time Station!" He turns to look at his cousin who has a look of sorrow. Mr. Conductor walks up to him and says "Junior, we can't leave without the Gold Dust." Junior begins to look at the ground with a sad face as Mr. Conductor walks up next to him and pats his cousin on the back.

"Aha! There's the blue puffball and it looks like he found the lost engine! Time to destroy!" shouts Diesel 10 as he slowly drives to where everyone is. Thomas looks over at Lady with a shocked expression and yells "Run, Lady! Hurry before Diesel 10 gets us!" Burnett jumps into Lady and says "Let's go, Lady. I won't let you down again." The purple train blows its whistle and proceeds to quickly drive forward. A few feet away, Aqua notices a flat cargo carrier and says, "I have an Idea!" She runs over to the carrier, hooks it up to the back of Thomas, and stands on it in her fighting position shouting "Now run!" Thomas proceeds to drive forward as Mr. Conductor shouts "Watch out for the Viaduct! It's dangerous!" This leads into a battle where Aqua will have to attack Diesel 10 from the flat cargo carrier during the chase sequence. When the battle concludes, Aqua detaches the cargo car and rides Thomas throughout the rest of the chase.

The viaduct is in the distance and Burnett looks down at Lady with a bit of confidence saying "Come on, Lady. We can do this." All three of the engines drive faster as they head towards the bridge. Lady runs through it first and successfully makes it as the middle of the bridge is slowly collapsing. Thomas makes it as well, but a few more bricks from the viaduct fall off in the process. Burnett looks over at Aqua and Thomas with excitement shouting "Well done everyone! Well done!" Diesel 10 runs on top of the railroad over the viaduct, but falls as the last of the bricks and pieces of track drop into the water below.

Everyone returns back to where Junior and Mr. Conductor are waiting. Aqua runs up to them saying "Diesel 10 is gone. He shouldn't bother us again." Junior replies "That's good. My cousin has figured out something about how we can get the Gold Dust back too!" They turn to look over at Mr. Conductor as he says "Burnett, can you please take some of the gold swirls off of Lady's wheels and bring them over here?" Burnett nods his head and runs over to one of Lady's back wheels. Mr. Conductor looks over at Aqua and asks "Aqua, can you please hold this for me and take it to the well over there?" He holds up a silver mining pan and points at the well that is a few feet away. Aqua nods her head, grabs the pan, and walks over to the well. Burnett walks up to Mr. Conductor and asks "What do you need me to do next?" Mr. Conductor responds by pointing at the well saying, "Go put the swirls in the pan." Burnett walks over to Aqua and places the swirls in the pan. They all look over at Mr. Conductor as he says "Now put the pan in the well and wash out the dirt." Aqua puts the pan in the well and takes it out after a couple of second. Mr. Conductor walks up next to her and says, "Now throw the swirls in the air."

Aqua tosses the swirls up in the air and Gold Dust appears. Everyone looks up with delight and excitement. Junior and Mr. Conductor fill their whistles with the magic. When their whistles are filled, Mr. Conductor looks over at Aqua and Burnett saying "Thank you two for all you've done. This island can stay in harmony because of you." Junior walks up to Aqua and says "Here! Hold out your key-shaped sword." Aqua summons her keyblade and Junior sprinkles some Gold Dust onto it. She looks up at Junior as he says "This is for helping us. Thank you, Aqua." Burnett jumps into Lady and says "I have to head back to Shining Time Station to make sure everyone else is safe. Farewell!" He waves at the others and Lady drives away. The woman looks over to see Junior blow his whistle and they both wave at each other. Mr. Conductor walks up to Aqua and says "Thank you again for everything, Aqua. You are a really useful person." The two of them shake hands while looking at each other with grateful smiles. Mr. Conductor jumps into the back of Thomas. The blue engine blows its whistle as it drives away. Aqua looks up at the sky with a smile and says "Terra. Ven. Thank you."

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