Casey Jr (from The Reluctant Dragon, Kronk's New Groove, and Dumbo) as Thomas # 1 (Both the main heroes)
Rustee Rails (from Little Tykes Land & Rustee Rails Rides Again) as Henry # 3 (Both wise, clumsy, and funny)
Montana (from Play Safe) as Gordon # 4 (Both proud)
Harry Hogwarts (from Harry Potter 1998 & 2011) as James # 5 (Both vain)
Tootle (from Little Golden Book Land) as Percy # 6 (Casey Jr and Tootle are both best friends, just like Thomas and Percy are)
Shelbert (from The Little Engine That Could "2011 film") as Toby # 7 (Both wise)
Bahia Train (from The Three Caballeros) as Lady # 16 (Both beautiful)
Cerberus (from The Little Engine That Could "2011 film") as Diesel 10
Samson (from The Brave Locomotive) and The Train (from AICP Minneapolis 2007) as Splatter and Dodge
Casey Junior's Coaches (extra Casey Junior's caboose) (from Dumbo) as Annie and Clarabel
Lightning Mac (from Cars) as Bertie # 42
Pedro (from Saludo Amigos) as Harold
Mario (from Super Mario Bros.) as Mr. Conductor
Luigi (from Super Mario Bros.) as Junior
Penny (from Inspector Gadget) as Lily
Princess Peach (from Super Mario Bros.) as Stacy Jones
Inspector Gadget (from Inspector Gadget) as Burnett Stone
Adult Tricky (from Star Fox) as Billy Twofeathers
Pinocchio (from Pinocchio) as Patch
Brain (from Inspector Gadget) as Mutt
Henrietta, Elsie, Flora's Tram Coach, and Victoria (cameo)
Cranky as Himself (cameo)
Butch as Himself (cameo)
King Koopa (from Super Mario Bros.) as Himself
Mickey Mouse as Sir Topham Hatt (not seen)
Minnie Mouse as Lady Hatt (mentioned)
George as Himself (cut from movie)
Flyng Scotsman, National Railway Museum Chocolate and Cream Coach, Blue and White Mk1s, and NER Saloon (from Michael Palin's Great Railway Journeys Episode 1 in 1980) as Engine No. 475 and Its Coaches
Casey Junior: (puffing along with Tootle following) I promise we'll get you home to your uncle, Penny.
Haystick Ball: Follow me, partner. Right this way to Bufferville. Just a walk in the park.
Tootle: We're going through, Lily.
Haystick Ball: You're on your own from here on in, little buckaroo!
Thomas and Emily: (together) Little engines can do big things! (Casey Junior races through the tunnel)
Casey Junior: It is dark, and cold, and bumpy, but we're not afraid.
Tootle: Casey, look, it's the missing coal!
Penny: Coal truck?! Stoke up the magic in the mountain! That's part of Super Mario's clue to the gold dust!
Casey Junior: And Penny, that's what you'll do with coal, and stoke it up to make steam. We shall be really reliable and help Mario. Let's go back for that coal truck.
Tootle: (while he and Casey buffering up to the coal truck from in front and behind) Buffers, coal truck, we're starting to solve the mysteries, Penny.
Penny: You two are really useful engines, guys. (The two engines are heading for the buffers and arriving at Muffle Mountain)
Casey Junior: Penny?! Where are we?!
Penny: Muffle Mountain, Casey!
Tootle: I think we're feeling a little dizzy. We can't go any further. Our wheels won't let us. (Tootle uncouples himself from the coal truck with Casey getting uncoupled from the coal truck as well)
Penny: Then I'll be back, Casey, I promise, and will find my Uncle.
Casey Junior: It's getting windy up here. (Penny leaves Casey as a gust of wind pushes Casey down the slope leaving the coal truck behind) Oh, bust my boiler!
Emily: We've left the coal truck behind and Tootle's gone back to Fantasyland!
Penny: Where's Uncle? Can you take me to him?
Pinocchio: Jump up.
Penny: How did you know he could count on me?
Thomas: Stop, wheels, stop! (Pinocchio and Penny are racing to Uncle Inspector Gadget to find them when Casey, Thomas, and Emily fall into another magic portal)
Inspector Gadget: Oh, Penny, I'm so glad to see you.
Penny: There's this island with talking trains. And they've said you might be there. But Mario is very sick and Luigi is in trouble and I've left Casey and his engine crew behind. Please help us.
Inspector Gadget: I'm hoping to, but nothing seems to work.
Penny: That's the lost engine from long ago? Now we can go back to the island and bring Mario and Luigi home.
Inspector Gadget: I can't make her steam. I've tried all the different coals in the valley.
Penny: Bahia Train? Is that her name?
Inspector Gadget: Yes.
Penny: Coal. Special coal from Fantasyland's island. Pinocchio, do you think you can get some coal from a coal truck at the top of the mountain?
Pinocchio: Splendid idea! (rushes off to get some coal)
Luigi: (still on Cerberus's engine roof) I'm sorry, Penny, I'm sorry for what I have done. I'll be responsible, also really useful, because I will be. And I will be! (Harry Hogwarts screams in terror as Cerberus stops in time as Luigi lands on Harry Hogwarts's roof instead) Harry Hogwarts.
Cerberus: (Luigi tries to blow his whistle, but fails) Oh... So you're losing your sparkles too, eh? (laughs evilly) So long, twinkle toes.
Luigi: It's empty.
Cerberus: Here we go.
Harry Hogwarts: Oh no. What are we going to do?!
Luigi: We'll think of something!
Cerberus: (laughs evilly) That's it!
Luigi: I'll find some more, Penny, I promise. If I'm going to be any help at all, it's now or never, I've got to use up the rest of this stuff!
Cerberus: Are you ready?
Harry Hogwarts: No, we're not.
Luigi: Harry, please, get us out of here!
Harry Hogwarts: Now we are! (Luigi blows his whistle and manages to get himself and Harry out of trouble)
Cerberus: What in the--?
Harry Hogwarts: Hooray!
Luigi: Bye, Harry!
Harry Hogwarts: Bye, Luigi! (Luigi sneezes)
Luigi: Sorry, I'd be late, bro, better late than never.
Mario: We're all out of gold dust, aren't we?
Luigi: Yes, we are. Hey, it's a wonderful day! I mean we're down but we're not out.
Mario: No, we're out, but we're not down.
Penny: Did G2 love Bahia as much as you do? Did she take a ride on her?
Inspector Gadget: G2 loved her because I loved her, but never took a ride on Bahia. I couldn't fix her in time. (Gadget and Penny shake hands together. Gadget, Penny, Brain, and Pinoke got on board Bahia's cab and began stoking some coal into the boiler. When Bahia gets up more steam, she blows her whistle and starts to move as her light shines bright like a diamond in the sky, and puffs happily away with her train of wagons)
Pinocchio: Penny, look! The railroad's getting its energy back!
Inspector Gadget: Well, Bahia Train, the lights are all green for now. Green for glory.
Penny: G2 would have loved this journey.
Inspector Gadget: Yes, she would, and now you're safe with me. (kisses Penny on the head)
Bahia Train: (gets her face and smiles) So, Gadget, you didn't forget about magic. It's safe inside you.
Penny: (when she, Pinoke, Gadget, and Brain see Casey, Thomas, and Emily coming up behind) It's them!
Casey Junior: You've found her and she's beautiful! (Bahia Train whistles and Casey does the same as well. Bahia Train comes out of the buffers and arrives to where Mario and Luigi are waiting)
Penny: We're on Fantasyland. Stop, Uncle, stop, Bahia Train. (Brain barks) Hello, Luigi. Hello, Mario. Super Mario, this is my uncle.
Mario: I'm glad you've managed to find your way back. Luigi, do you realize who this is?
Luigi: I reckon this is one beautiful engine. Wow... This is the lost engine. Boy, are we glad to see you?! Now we can go back to Shining Time!
Mario: Luigi, we won't make it back to Shining Time without our gold dust. Without it, the magic can't excist. (Luigi looks stunned and sobs uncontrolably as Mario tries to comfort him)