Sakura is the princess of Clow Kingdom, which is ruled by her older brother, King T?ya. 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 disintegrate into feathers, which are scattered across dimensions. The High Priest of Clow Kingdom, Yukito, immediately realizes that Sakura's "feathers" were the manifestation of her soul and memories; without them, she will die. In order to save Sakura, Syaoran must journey to retrieve her wing's feathers, the fragments of her memories.
Yukito sends Syaoran and the unconscious Sakura to the Dimensional Witch, Y?ko, who is one of the main characters in xxxHolic. There he meets Kurogane, a rough-mannered ninja banished from his world by Princess Tomoyo, and Fay D. Flourite, 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 Ginry?, and for Fay, it is the tattoo on his back which regulates his control of his magic. 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 Y?ko, because what Sakura values most are her memories of and with Syaoran.) Only when the three agree to her terms does Y?ko 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.