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Sakura is the princess of Clow Country, which is ruled by her older brother, King Toya. Her childhood friend Syaoran is a young archeologist. 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. When Sakura goes to the ruins to confess her love for Syaoran, she spots the symbol and recognises it. 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 Witch of Dimensions, Yuko.There he meets Kurogane, a rough-mannered ninja banished from his world by Princess Tomoyo, and Fai D. Florite (or Fai D. Flowright, or
other combinations of Fai/Fye/Fay and Fluorite/Flowright), 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 taken an oath that prevents him from using 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 the rest 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 pocket-sized version of Magic Knight Rayearth's Mokona.
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.