In 1999, Shiro Kamui returns to Tokyo for the first time in six years to honour his mother's final wishes. It is here he will fulfill his destiny, yet all he wants is for others to leave him alone. According to the yumemi Hinoto, Kamui alone has the power to decide the world's fate, which depends on whether the kekkai which exist in Tokyo remain standing.
Kamui must decide to either become a Dragon of Heaven (also known as the Seven Seals) and protect humanity from supernatural destruction or join the Dragons of Earth (also known as the Seven Angels) to destroy humanity so the Earth can be reborn. While Kamui couldn't care less about the world, he feels he must protect childhood friends Fuma and Kotori, Fuma's younger sister. However, his choice to become a Dragon of Heaven results in tragedy when Fuma is revealed to be Kamui’s “Twin Star”, destined to be Kamui’s opposite number no matter which side Kamui chooses.
Kamui must reluctantly fulfill his destiny alongside his allies, the Dragons of Heaven, whose destinies are also ostensibly foreordained. They all soon learn the tragedy of loss and the painful price of victory. To save the world, Kamui must become certain of his resolve and of what he truly desires for himself, Fuma, and the world.
Sakura is the princess of Clow Country, which is ruled by her older brother, King Toya. Her childhood friend Syaoran is a young archaeologist. Sakura is revealed to have strange powers when she has a vision of a mysterious symbol and places she has never seen. Meanwhile, Syaoran discovers the same symbol at the ruins he is excavating. He sees Sakura standing on the symbol on the ground. Ghostly wings appear on her back and a mysterious force begins to pull her into the walls of the ruins. Syaoran rescues her in time, but her wings are scattered across dimensions. The High Priest of Clow Country, Yukito, immediately realizes that Sakura's "wings" were the manifestation of her soul and memories; without her wings, she will die. In order to save Sakura, Syaoran must journey to retrieve Sakura's lost memories.
Yukito sends Syaoran and the unconscious Sakura to the Dimensional Witch, Yuko, who is one of the main characters in ×××HOLiC. There he meets Kurogane, a rough-mannered ninja banished from his world by Princess Tomoyo, and Fai D. Flowright (as spelled in Clamp's official guide or "Fai" as translated by Del Rey), a magician who fled his world to avoid King Ashura. Each of them must pay with what he values most in order to gain the power to cross dimensions. For Kurogane, it is his sword Ginryu, and for Fai, it is the tattoo on his back which regulates his control of his magic. (Fay later reveals that he still possesses magic, but has sworn not to use it without the tattoo on his back.) Syaoran, on the other hand, must pay with his relationship with Sakura: even if he is able to retrieve all of her memories, she will never remember anything about him or their relationship. (This sacrifice also pays Sakura's "toll" to Yuko, because what Sakura values most are her memories of and with Syaoran.) Only when the three agree to her terms does Yuko present them with the power to cross dimensions; a white creature named Mokona Modoki.
While traversing through worlds to find Sakura's feathers, the four travellers and Mokona are forced to overcome many dangers and opponents, some of whom are figures from Syaoran's past who wish to collect Sakura's feathers for their own reasons as they are seen to be objects that hold great power.