Master Tyrone teaches Austin to make "The Great Pie" for Empress Tasha. But after he does, ninja Uniqua and Pablo try to steal it!
Tyrone is shown in the backyard wearing a white, puffy baker's hat and carrying a brown, wooden spoon. "Pie-ya!" he shouts repeatedly. He introduces himself as Pie Master Tyrone, a resident of Japan who makes pies like a samurai. He sings Samurai Pie. After the song, Austin appears in the backyard. "Pie-ya!" they shout to one another, making karate poses. At first, Tyrone thinks Austin is a ninja, but Austin tells him that he's come to him to learn how to make pies. Tyrone accepts Austin as his student, and Austin thanks him. Under Tyrone's direction, the two head off to Ancient Japan. The backyard transforms into the grassy landscape of Japan as Tyrone, now dressed in a complete pie-making uniform, consisting of a white tunic and pants, heads to the bakery. On a hillside, he meets up with Austin, his current student. Austin is also dressed in a white tunic and pants, but he doesn't have a baker's hat. Both Austin and Tyrone sing a reprise of Samurai Pie. Austin asks Tyrone when he will get to wear a baker's hat with his outfit. "Patience, Young Austin." Tyrone tells him calmly. "Only when you have mastered the art of making pies can you wear the puffy hat." Tyrone tells Austin that today, he will complete the task of creating a pie for the Empress of Japan, Tasha. The two head to the palace of Empress Tasha.
Meanwhile, Uniqua, who is dressed in a ninja outfit, drops from the sky and lands on her feet. She happily greets the viewer, and explains that ninjas are sneaky and quiet, and they always land on their feet. Just then, Ninja Pablo drops from the sky and crash lands in a bush. "Well, almost always..." admits Uniqua. Together the two ninjas set off for the palace to snatch some pies.
Once they arrive at the palace, Tyrone informs Austin that they must take the secret passageway to the bakery, because the main entrance is guarded with traps. Tyrone opens a trapdoor and leads Austin down a ladder and through an underground path adjoining the palace to the bakery. At the bakery, Tyrone hops out of the trapdoor and Austin looks around the room excitedly. Tyrone then demonstrates for Austin how a pie is made. Austin watches in awe as Tyrone flies through the air, grabbing a wooden spoon from the wall behind, then jumping to a shelf to grab a pie tin. He launches it into the air. Tyrone jumps onto the preparing table and masterfully rolls out a pie dough with his feet. He does a back flip and slices the pie dough in half, then tosses both pieces in the air. He quickly stirs some pie filling and launches it in the air as well. With a great leap in the air, Tyrone catches the pie tin and lands on the floor. With three quick movements, Tyrone catches the bottom layer of dough, the filling, and the top layer of dough with the tin. Tyrone now holds a perfect pie in his hand.
Austin, who is overjoyed by his master's skillfulness, quickly grabs a spoon and shouts "Pie-ya!", eager to start making pies, but Tyrone grabs the spoon from him. "Young Austin, before you can make pie, you must learn to make pie, and to learn to make pie, I must teach you to make pie." Tyrone tells him firmly. Tyrone then begins training Austin how to make pies. He and Austin sing the song titled Do You Wanna Make Pies? as Austin repeats several exercises, including touching a pie tin with a rolling pin, mixing a bowl of filling and kicking his foot, and turning around while filling a row of pie tins with pie filling. Suddenly, a gong sounds and Tyrone informs Austin that the sound means that the Empress wants pie. The two pie-makers set off for the palace. Meanwhile, Ninjas Uniqua and Pablo scale a stone wall just outside the palace.
At the palace, Tyrone greets Tasha, who is sitting at a table in the room. Meanwhile, Ninjas Uniqua and Pablo are watching everything from the window. Tyrone tells the Empress that he will challenge his current student, Austin, to make whatever pie she wants. Austin suggests she would like the Great Pie, a legendary pie that only the greatest pie-maker can create. Tyrone is petrified, but the Empress agrees with Austin and thinks it's a marvelous idea. The ninjas get excited after overhearing this. Tyrone, Tasha, and Austin sing The Great Pie. During the song, the ninjas sing along, but the others take no notice of them. They run off. Tyrone and Austin are next shown walking back to the bakery.
At first, Austin thinks that he and Tyrone will make the Great Pie together, but Tyrone tells Austin that since making the Great Pie was his idea, he shall make this pie by himself, but he also tells him that this is his true test in becoming a master pie-maker. "Make the Great Pie!" he declares. Austin rises to the challenge. He first creates a small pie that Tyrone ejects and throws into a pile of previous failures. Tyrone tells Austin to make a better pie, the Great Pie, next time he attempts to bake a real pie. The camera moves to ninjas Uniqua and Pablo, who are at the bottom of the hill that the bakery stands on. They start sneaking up the hill to steal the pie Austin will make, but set off a trap. Pie tins are shot in Uniqua and Pablo's direction.
Uniqua decides to duck under the tins, and Pablo does so as well. The two are now farther up the hill. Tyrone and Austin are next shown. Tyrone tells Austin to create a larger pie than his previous. Austin does so, but Tyrone inspects in and ejects the pie. This happens repeatedly. Uniqua and Pablo are next shown. They have set off another trap, that features rolling pins that roll down the hill toward them. Uniqua decides to jump over them and Pablo does too, but after a few jumps, Uniqua and Pablo each land on a pin that rolls them back down the hill. Uniqua and Pablo fall a few times and are not able to get up the hill. They come across two trees.
In order to get to the bakery, they will have to jump from tree to tree until they reach the building, avoiding the pins below. Uniqua tries to get to the trees' top, but falls. Pablo attempts, and fails as well. The two sing Ninjas Like Pie Too as they jump from tree to tree and reach the bakery window. Meanwhile, inside of the bakery, Austin has created a large pie Tyrone claims to be the Great Pie. Tyrone places it on a tray on top of a wheel cart and is about to bring it to the empress when Uniqua and Pablo enter to steal Austin's masterpiece. Tyrone flings Austin's many smaller pies at the ninjas, covering them in blueberries and pie crust.
Uniqua and Pablo take action and lunge forward. Tyrone moves the pie out of their reach. They start to throw pies, covering Tyrone and Austin in pies. With all of the commotion, the pie is flung out of the bakery and into the Japanese palace. The four run to the palace. Inside, Tasha yells "WHERE'S MY....". The pie comes through the window and on to the table where Tasha is sitting. "...pie?!" Tasha finishes in suprise. She is pleased and takes a fork to take a bite of the pie. She does so, and tells Austin and Tyrone that the food is the most wonderful pie she has ever tasted. The cast sings The Great Pie again, during which, Tyrone gives Austin his very own baker's hat.
Pablo's stomach rumbles. Tyrone asks if the sound was more pie-stealing ninjas. Pablo tells him that it was just his stomach and invites the others to his house for some milk to go with the Great Pie. The five rush to Pablo's house as Japan transforms back into the backyard. The characters sing the end song and head to Pablo's for a snack. Tyrone opens the previously closed door and shouts "Pie-ya!". The end credits begin.