The story of Yakitate!! Japan starts with a look at how Azuma became motivated to become a baker. Ten years ago, in his small hometown, Azuma was dragged to a local bakery by his sister. There he meets the store owner who made him realize that it's possible to appreciate bread in a town that grows rice as it's main source of living. The store owner teaches him how to make bread that his family will also like and he realizes that Azuma is in possession of "solar hands", a rare gift to bread artisans that helps speed up the yeast fermentation in bread. But in the end, spurred by Azuma's drive to make his grandfather appreciate bread too, the baker closed shop to go to Tokyo and pursue his own dream of creating Japan. Through the years, Azuma took in his mentor's dream and now is also trying to make bread that will represent Japan. After that the story could be divided into four major arcs with each arc revolving around a competition and interspersed with a few short stories in between.
Pantasia Entrance Examination
When Azuma went to Tokyo in order to join the main Pantasia Bakery branch, he instead finds out that he needs to win the Pantasia Entrance Exam in order to join the main branch. There he meets Kawachi Kyousuke, another baker aiming to join the main Pantasia branch, Suwabara Kai, the guy who is expected to win the competition, Azusagawa Tsukino, one of the granddaughters of the owner of Pantasia, and the judge Kuroyanagi Ryou. In the end though due to Azuma caring about Kawachi's siblings and him being gullible to Kawachi's sneaky side, Azuma backed out of the competition in order for Kawachi to get in. When Kawachi learned about this, he backed out too and both of them were hired by Tsukino for the Pantasia Southern Tokyo store.
At the Southern Tokyo store, they meet the store manager, Matsushiro Ken, the one who bakes the best French bread in Japan. In order for them to be able to place the bread they make into the store, the manager told them to bake a bread that even a horse would eat. Though in the end only Kawachi's bread was the one that was eaten by the horse, the manager was still amazed by Azuma's bread and told him that he exceeded his expectations.
While the main branch of the Pantasia Bakery was creating so much commotion, the Southern Tokyo store on the other hand is dying. And the main cause of it is their rival store just right across the street, the St. Pierre Bakery. When St. Pierre was going to announce their new bread through a TV show, the manager of St. Pierre, Mokoyama Tsuyoshi, and Ken agreed that it would be a new bread duel where both St. Pierre and Pantasia would present their new product to a set of judges. It ended on a draw but Pantasia's bread was more of a hit since it was being sold free.
Pantasia Newcomer's Battle
The Pantasia Newcomer's Battle is a battle among all the new employees of all the 128 Pantasia stores to know who's the best among them. The winner gets 1 million yen a chance to study for 3 months at France together with the runner-ups and a chance to work at the main branch. Being among the new employees, both Azuma and Kawachi gets to join in the battle. There, they meet other new Pantasia bakers like Azusagawa Mizuno, Shachihoko, and the former St. Pierre manager, Mokoyama, dressed in a koala mask. In the final round, the match was between Kanmuri Shigeru and Azuma for the first place while it was Kawachi and Kai for third place. It ended with Azuma winning first place, Shigeru placing second and Kawachi and Kai tieing for third place. Since Shigeru had been to France already, he gave up his France trip to Kawachi. Kawachi then chose to work at the main Pantasia branch while Shigeru chose to work for the Southern Tokyo branch. Shigeru then told the Southern Tokyo branch people that an imminent takeover of St. Pierre over Pantasia is about to take place with Azusagawa Yukino holding almost 40% of Pantasia's stocks. Shigeru's plan to defeat Yukino is to let Azuma and the gang participate in the upcoming Monaco Cup while they were in France and make 10 billion yen by gambling in the outcome of the competition.
Azuma, Kai and Kawachi, accompanied by Kuroyanagi, flew to France and there, they met Meister Kirisaki's sister, Sophie. Sophie took on the task of training the three in order to make bread that would fit the taste of Europeans and also in order to defeat the Kaiser brothers in the Monaco Cup. In the preliminaries, there were 135 countries participating. It was narrowed down to eight and then later to four for the semi-finals where Japan was pitted against the crowd favorite, France. The final match was between United States and Japan. And though the battles throughout the competition were rigged against Japan even with the judge, Pierrot Bolneze, being just and fair, Azuma, Kawachi and Kai still won the Monaco Cup. When the tournament ended and everyone is celebrating, Monika, the pastry chef from the USA team arrived and told them that St. Pierre and Pantasia is now owned by one person. Kirisaki Yuuchi, the new owner of both stores and holding more than 50% of the companies' stocks challenged them to a new competition, the Yakitate!! 25. They'll put their Monaco winnings at stake against all of Kirisaki's stocks. Tsukino, the new president of Pantasia under the new owner, agreed to Kirisaki's challenge.
Yakitate!! 25 is a televised competition where the challenge is played in an 5x5 go or othello board. Each square represents a town in Japan and the challenge is to make a bread that uses the chosen town or area's specialty. Azuma's team is challenged both by new characters like CMAP, Tsutsumi Kanmuri, Miki Norihei as well as old ones like Kai and Monika, Mokoyama, Yukino and even Meister Kirisaki.