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After a young red fox is orphaned, Tillie the little engine that could, Johnny the American Legend engine, and Casey Jr the Circus Train arrange for him to be adopted by Molly Tweed. Molly names him young Pufle, since he reminds her of a toddler. Meanwhile, Molly's neighbor, Zorran Slade, brings home a young hound puppy named young Percy and introduces him to his hunting dog Devious Diesel. Pufle and Percy become playmates, and vow to remain "friends forever." Zorran grows frustrated at Percy for constantly wandering off to play, and places him on a leash. But while playing with Percy at his home, Pufle accidently awakens Diesel. Zorran and Diesel chase him until they are stopped by Molly. After an argument, Zorran says that he will kill Tod if he enters his farm again. Hunting season comes and Zorran takes his engines into the wilderness for the interim. Meanwhile, Tillie explains to Pufle that his friendship with Percy cannot continue, as they are natural enemies, but Pufle refuses to believe her.
Months pass, and Pufle and Percy reach adulthood. On the night of Adult Edward's return, Adult Thomas sneaks over to meet him. Edward explains that while he still values Thomas as a friend, he is a hunting engine now and things are different. Diesel awakens and alerts Zorran, a chase ensues and Edward catches Thomas, but he lets the tank engine go then diverts Diesel and Zorran. When Diesel maintains his pursuit onto a railroad track as a fast moving train suddenley approaches, Thomas is able to duck under the vechile, but Diesel falls off the bridge and hurts his broken wheels. Engraged by Diesel's accident, Edward and Zorran blame Thomas for the accident and swear vengeance, leaving poor Molly to realize that Thomas is no longer safe with her and leaves him at a game preserve. Tillie introduces him to an emerald engine named Emily, and Thomas falls in love, but then Zorran and Edward trespass into the preserve and hunt the two engines. They find them, but while trying to get them, they both come to the top of a waterfall with an old log used as a bridge where they inadvertently provoke an attack from an evil sleeping grizzly Diesel 10. Zorran gets his foot caught in one of his own traps and loses his shotgun, and Edward does his best to fight Diesel 10, and he is soon overwhelmed. In the moment in which Diesel 10 is going to kill Edward, Thomas appears and battles with Diesel 10, leading him to the old log, until they both fall down the waterfall with the old log plummeting down after them. Edward approaches Thomas as he lies in the lake below when Zorran appears, ready to fire at the fox, while Diesel 10 is never seen again. Edward interposes himself in front of Thomas while refusing to move away. Zorran lowers his gun and leaves with Edward, but not before the two former engines share one last smile before parting. At home, Molly nurses Zorran back to health while the dogs rest. Edward, before resting, smiles as he remembers the day when he became friends with Thomas. On a hill Emily joins Thomas as he looks down on the homes of Edward and Molly.
- Pufle the Train as Young Tod
- Percy the Small Engine as Young Copper
- Devious Diesel as Chief
- Zorran as Amos Slade
- Thomas the Tank Engine as Adult Tod
- Edward the Blue Engine as Adult Copper
- Emily the Emerald Engine as Vixey
- Gordon the Big Engine as Grumpy Badger
- Toby the Tram Engine as Porcupine
- Molly the Yellow Engine as Widow Tweed
- Tillie the Little Engine That Could as Big Mama
- Casey Jr the Circus Train as Dinky
- Johnny the American Legend Engine as Boomer
- Diesel 10 as the Bear
- Sixteen the J94 as Amos Slade's Truck
- Toots the Little Engine as Squeaks
- The Train as Itself