Thomas and Twilight Sparkle's Adventures of Jonah: A Veggietales Movie is a T&F/MLP/Big idea crossover to be made by Stuingtion.
Bob the Tomato is driving Dad Asparagus and some of the Veggie children to see the popular singer "Twippo" in concert. Meanwhile, Laura Carrot taunts the other children because she won a backstage pass. Her taunting makes Dad Asparagus accidentally hit Bob, who loses control of the vehicle. Laura loses her backstage pass as the vehicle loses control and careens down a hill, stopping short of a river.
In a nearby restaurant, Bob blames Dad Asparagus for crashing the car, and Junior blames Laura. Junior is met by the Pirates Who Don't Do Anything, who say that he is tough on his friend and encourage him to show some compassion. To illustrate, they begin to tell all the Veggies a story.
Jonah is a Prophet from Israel who goes from town to town delivering God's messages. One night, God asks him to leave Israel and deliver a message to Nineveh, a rough and dangerous city in Assyria, and known for behaving badly and slapping others with fishes; Jonah panics and tries to flee from the Lord. He goes to his travel agent, Angus, who tells him that the farthest he can get from Nineveh is Tarshish. He asks the Pirates in the harbor to take him to Tarshish. They resist, but Jonah convinces them by paying them. On the way, a guilt-stricken Jonah goes below deck to rest. There, he meets Khalil the Caterpillar, a traveling Persian rug salesman.
After having a nightmare of running from God, Jonah finds the ship beset by a great storm. Captain Pa Grape concludes that the storm has been sent because God is angry at someone on the ship. They all play Go Fish to determine who it is. Jonah loses the game and admits that he is running from God, then is forced to walk the plank; with Jonah off the ship, the skies clear immediately. The Pirates attempt to reel him back in, but a whale swallows Jonah. The Pirates are forced to use a bowling ball with Khalil inside it as ammo. The whale swallows the ball, disgorges the lifebelt, and swims away.
Inside the belly of the whale, Khalil finds Jonah saddened that he is going to die for disobeying God, but they are visited by a host of God's angels, who explain through a rousing number that if Jonah repents, then God will grant him a second chance too. He and Khalil are spit up onto the shore where they ride his camel, Reginald, to Nineveh.
After Jonah is denied entrance to the city, the Pirates appear, explaining that they spent all the money Jonah gave them on Mr. Twisty's Twisted Cheese Curls and won a sweepstakes, giving them free access to Ninevah where the Cheese Curls are produced. They sneak Jonah into the city disguised as sweepstakes winners, though they are all promptly arrested after Larry steals the King's Cheese Twists. After being sentenced to death, they are granted an audience with King Twistomer. When King Twistomer hears that Jonah has survived in the belly of a whale, he listens to his message. Jonah delivers the message given to him by God, then tells them that they should repent and amend their ways, or Nineveh will be destroyed; King Twistomer and the Ninevites quickly repent.
Still expecting the Ninevites to be destroyed, Jonah watches and waits from a distance. Khalil is disappointed in Jonah, and tries to explain to him that God is compassionate and merciful; but Jonah, who is feeling pathetic and self-important, cannot accept that. The story ends with Khalil and Reginald leaving Jonah on a cliff overlooking the city.
Back in the present day, the Veggies are disappointed in the anticlimactic ending but come to understand the point of the story: God wants everybody to show compassion and mercy, even to those that do not seem to deserve it. Twippo appears in the restaurant unexpectedly and offers to give everybody a lift to the concert, while Bob forgives Dad Asparagus and Junior gives his Twippo ticket to Laura. The film ends with a grand musical number and the arrival of the tow truck driver, who bears a striking resemblance to Khalil.
- 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.