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Cranky Kong is on holiday and leaves Thomas the Tank Engine to take care of Mario and his friends. When Bowser returns with his Koopalings, with the help of Diesel 10 and Smelter (a made-up TUGS character), to destroy a lost engine named Isobel, who crashed in a bad accident. It's up to Mario, Thomas, Rosie, James, Duck, Barney and BJ to get Isobel back to life, and stop Bowser, his Koopalings, Diesel, Zorran, Diesel 10 and Smelter.
Super Mario Bros
- Mario (played the role of Thomas)
- Diddy Kong (played the role of Henry)
- Donkey Kong (played the role of Gordon)
- Wario (played the role of James)
- Green Toad (played the role of Percy)
- Toad (played the role of Toby)
- Bowser (played the role of Diesel 10)
- Bowser Jr (played the role of Splatter)
- Larry Koopa (played the role of Dodge)
- Roy Koopa
- Wendy O'Koopa Jr.
- Morton Koopa
- Iggy Koopa
- Ludwig von Koopa
- Lemmy Koopa
Thomas and Friends
- Thomas (played the role of Mr. Conductor)
- Edward (cameo)
- Henry (cameo)
- James (played the role of Junior Conductor)
- Percy (played the role of Patch)
- Roise (played the role of Lilly)
- Duck (played the role of Burnett Stone)
- Emily (played the role of Stacy Jones)
- Diesel 10 (played the role of P.T. Boomer, he was only seen on the original script of the T&TMR movie)
- Gordon (played the role of Billy Twofeathers)
- Smelter the Diesel Tug
Barney & Friends
- Baby Bop
New Character (later appearing on Thomas and Friends The Trackmaster Series
- Barney has his Season 3 voice and 1995 costume.
- Baby Bop has her Season 3 voice and 1996 costume.
- BJ has his Season 3 voice and 1996 costume.