Masamoto Tenno, the oldest son of Masamoto Takeshi, is killed in 1609 in Toba by the ninja Dokugan Ryu, also known as Dragon Eye. Two years later a ship, the Alexandria, is caught in a storm along the Japanese coast. On board is Jack Fletcher, a 12-year-old English boy. When the ship hits a coral reef and is shipwrecked, his father, John Fletcher, who is pilot, sails the ship into a bay. There, the crew attempts to repair the ship as fast as possible, fearing an attack by the Wako, ruthless Japanese pirates. When the ship is ready to sail again, someone spots a pirate ship in the distance. That night all lights are out. Jack doesn't feel at ease and takes a look on the deck. There he sees men dressed in black and hurries to warn his father. His father tells him to stay in the cabin until he comes back, but when Jack hears his father scream he runs to the deck. There his father is surrounded by men dressed in black. One of them takes Jack and threatens to kill him unless John tells him where the rutter is. John tells them in the hope they will let his son live. When they are about to kill Jack, John manages to save him, but gets killed himself. As he is dying he tells Jack to take the rutter before the ninja can find it and escape from the ship. Jack manages to find the rutter but is confronted by the ninja who killed his father. Jack tries to escape and when he reaches the deck, the ship blows up, throwing him into the ocean. Jack is found by Masamoto Takeshi and taken to his sister Hiroko's house. There Jack is treated. After a few days living in the house, Jack grows unhappy and tries to escape. He fails and is caught by Taka. He also meets Akiko, the daughter of Hiroko.One day Masamoto Takeshi interrogates him through a translator, a Portuguese priest named Father Lucius. When Jack tells them about the murderer of his father, Masamoto realises it is Dokugan Ryu. Masamoto feels guilty towards Jack for not being able to kill the ninja, so he adopts Jack as his son until he has grown up. He also returns the rutter to Jack, seeing it is important to the boy. The Portuguese priest is curious about the book, but Jack lies to him about it, saying it is his father's diary. The Portuguese priest is ordered to teach Jack Japanese. Not much later Masamoto leaves to Kyoto because his school needs him. He leaves his youngest son Yamato in Toba so he and Jack can become friends, though Yamato clearly doesn't want to be. When Yamato is practising with a wooden sword called "Bokken", Jack sees his chance to learn how to fight with a sword and asks Yamato to teach him. Yamato agrees. They compete and Yamato always wins. When Jack finally manages to get a draw, he is called to Father Lucius, who is dying. Lucius reveals to Jack that someone is after him. Later, Jack tells Akiko about what father Lucius had said. Akiko advises him to tell someone, but Jack decides against it, because he thinks nobody would believe him. A samurai comes with a message saying that Masamoto will return to Toba soon. The evening before Masamoto's arrival, the house is attacked by ninja, including Dokugan Ryu. Dokugan Ryu asks Jack where the rutter is, but Jack keeps quiet.Dokugan Ryu manages to kill a maid before Masamoto arrives, forcing him and his ninja to flee. The next day, Masamoto takes Jack, Yamato and Akiko to Kyoto so they can learn the way of the samurai at his school. There Jack makes of Oda Kazuki. When Kazuki attacks Jack with the help of students from another school they are stopped by Masamoto and Kamakura Katsuro, the head of the Yagyu-ryu School. Kamakura challenges Masamoto to a Taryu-Jiai and Masamoto agrees. Later Masamoto is furious at Yamato for not helping Jack and the others. Upset, Yamato leaves the school and joins the Yagyu-ryu. When it is time for the Taryu-Jiai, Yamato turns out to be one of the opponents of the Yagyu-school. When it ends in a draw, Yamato and Jack are to compete against each other for the victory of the school. Whoever gets the Sword of Jade and takes it back to school wins. It is a close race, but when they are climbing next to the waterfall, Yamato can't go on and accuses him of taking away his father. Jack, who has taken the sword, says he never wanted to do that and tries to help Yamato. But Yamato refuses to listen and jumps in the waterfall. Jack jumps after him and manages to save him. Yamato apologises and asks him to be friends again. Jack agrees. When they come back at school, Yamato carries the sword. He is about to give sword to Kamakura, but in the end he gives it to his father, admitting it was Jack who took the sword. Masamoto then tells Yamato that he has what it takes to be a student of his school and a Masamoto. Some time after the Taryu-Jiai the Gion Matsuri Festival takes place. Jack spends the days with his friends and has a great time until he walks into a man dressed in black. The man tells him to go away and Jack recognises him as Dokugan Ryu. Together with his friends he follows the ninja into the Nijo-castle. There he stops Dragon Eye before he can kill Daimyō Takatomi. Masamoto rewards Jack and his friends for his bravery, giving Jack his first swords as a gift.