Thomas and Twilight Sparkle join The Pirates Who Don't Do Anything: A Veggietales Movie is a T&F/MLP/Big idea crossover to be made by Stuingtion.
Somewhere in the late 17th century, two pirate ships are fighting, while Alexander of Monterria is captured by Robert the Terrible; the other pirates search the ship for Eloise, but miss her hiding spot and leave. When Eloise and Willory emerge, she sends a device that her father made, a "Helpseeker," to find heroes to save Alexander. It evades the pirates on the ship and jumps into the sea.
Meanwhile, George, Sedgewick, and Elliot are working at a dinner theater. Sedgewick has invented a remote-controlled toy truck with a claw arm to help him do things he does not feel like doing - though when Ellen asks him to get her some barbecue sauce, it is out of range of his toy and he refuses to make the effort himself. Elliot has a list of things he is afraid of, and when Bernadette asks him to get the barbecue sauce, he says the back room is dark and therefore "on his list." George does what everyone tells him; his children, George Jr. and Lucy, idolize the star of the show, Sir Frederick, and he is worried he does not impress his kids.
Elliot, Sedgewick, and George want to be seen as heroes by their loved ones, but since they are only cabin boys, they think their dream is unattainable. After the show, while they are cleaning up, an old blind man appears out of nowhere. They audition but it backfires and messes up half of the restaurant; as a result, they are fired and thrown into the alley, where they find the Helpseeker and are teleported to the 17th century.
Meeting Eloise and Willory, they set off to Jolly Joe's where they learn it is Robert who has kidnapped the prince in the hopes of exacting revenge on the king and the clues to find Robert's fortress are hidden in a cave past the Rocks of Malabar. They do find the clues there, but Sedgewick happens across what appears to be a pool of cheese curls, and decides to stay on the island and relax instead of pursuing Robert. When George and Elliot return to the beach, they discover Robert's men have taken their boat and captured Eloise and Willory; they head out to follow the clues.
Back in the cave, the cheese curls turn out to be alive - and vicious. Sedgewick is attacked and discovers he can do anything without giving up. When George and Elliot get to the isle, the rocks start to surround them, but then Sedgewick arrives, having now swum across the ocean followed by the cheese curls. The rocks find the curls amusing and start to interact with them.
The pass opens and one of the rock-monsters helps them get through it. Within the hidden bay, they quickly find Robert's fortress, which is apparently unguarded, but a giant serpent attacks their ship. George and Sedgewick are terrified, but Elliot realizes the guardian is actually a mechanical device; when it "eats him," he is able to shut the machine down from inside and save his friends.
They rescue the prince and princess, with the help of Sedgewick's "labor-saving device," only to be stopped by Robert. Finding his self-respect at last, George uses a chandelier to knock Robert down. They escape through the fortress's cistern, with Robert in hot pursuit. Back in the bay, Robert's ship opens fire on the heroes, but the king shows up just in time, and Robert goes down with his ship.
The king gives them medals for their good work, reminding them heroes are not necessarily strong, handsome or dashing, but in fact anyone is right no how matter hard the situation. The Helpseeker returns them to the restaurant, just in time for the Friday night show, but Robert has stowed away on their trip back and attacks Sir Frederick, mistaking him for George; a final showdown with Robert sends him back to his own time. The audience cheers wildly, including their loved ones, and George's children respect him at last. Offered a second chance to be in the show, they refuse, saying life has plenty of adventure of its own... as the Helpseeker blinks once again.
- Zecora, Stephen, Sharky, Mako, Willy, T.C., Hugs, Sherin, J.J., Evan, Steamy, Puffy, Rattlesnake Jake, Dusty Crophopper, Ishani, Timber, Splinter, and Chomper, Falcon, Anna, Elsa, Wreck-It Ralph, Vanellope von Schweetz, guest star in this film.