The series starts by introducing childhood friends Syaoran, a young archaeologist who is investigating a ruin from Kingdom of Clow, and Sakura, the princess of the Kingdom of Clow, daughter of the late king Clow Reed. When Sakura visits Syaoran in Clow's ruins, a pair of ghostly wings grow from her. The wings disintegrate into feathers that scatter across dimensions. The High Priest of the Kingdom of Clow, Yukito, realizes that Sakura's "feathers" were the manifestation of her soul, and that they grant her the power to cross dimensions; but without them, she will die. Yukito transports the two to the world of the Dimensional Witch, Yūko Ichihara; Syaoran begs the witch to help to save Sakura.

Syaoran meets two people who also have a wish: Kurogane, a rough-mannered samurai who wishes to return to his home after being banished from his world by Princess Tomoyo in order to learn what true strength is; and Fai D. Flowright, a magician who wishes never to return to his world so he can avoid meeting his master, Ashura-ō. Before she will grant the power to cross dimensions, Yūko demands that each must pay with what they value most. Kurogane pays with his family's heirloom, the sword Ginryū. Fai pays with the tattoo on his back that suppresses his magical power. Syaoran pays with his relationship with Sakura; even if Syaoran is able to retrieve all of Sakura's memories, she will never remember him. When the three agree to her terms, Yūko presents them with a white creature named Mokona Modoki that holds the power to cross dimensions. The group then set out on their journey across dimensions in search of Sakura's feathers. As the first feather is obtained, Sakura awakes from her catatonic state, without any memories. During their adventures, the group learns that the feathers have various effects and bestow abilities to those who hold them in the various dimensions, which sometimes makes retrieval difficult. They are unknowingly observed by a powerful wizard, Fei-Wang Reed, who wants Sakura's feathers for his own agenda. Although the group obtains more feathers, they do not help Sakura remember events related to Syaoran. She begins bonding with him regardless. The group of five also start befriending each other to the point where Fai jokingly labels them as relatives.

In the journey, it is revealed that Syaoran is actually a clone who holds half of the heart of the original one. Various years ago, the original Syaoran was taken prisoner by Fei-Wang, who created the clone to collect Sakura's feathers. Before being imprisoned, the original Syaoran sealed a part of his own heart within his clone, hoping he would grow emotions. However, as the seal is broken, the clone becomes emotionless and who betrays the group. Once freed from Fei-Wang's prison, the original Syaoran joins Sakura, Fai, Kurogane, and Mokona in their journey, with Sakura deciding to search for a way to save the clone. Sakura foresees a future in which Fai kills the original Syaoran due to a curse Fei-Wang placed on him, and is able to modify it to become the victim. As a result, Sakura's soul leaves her body and enters the Dream World, while the others seek a way to get there. When transported into the Dream World with a feather, Syaoran faces his clone, who wants his feather. As both Syaorans attempt to finish each other, Sakura intervenes, receiving the clone's blow. Before her soul disappears, Sakura reveals that she is a clone from the original Sakura, who was also taken prisoner by Fei-Wang. Sakura's soulless body is then taken by Fei-Wang, who wishes to use its stored power. Learning that Fei-Wang is in a Kingdom of Clow whose time was halted, the group departs to rescue the two Sakuras.

As they arrive in Clow, the original Syaoran explains to his partners the origins of his and Sakura's clones: as a young child, Syaoran went to the Kingdom of Clow, as his mother had foreseen the future, which involved him in such a world. There, Syaoran met the original Sakura, and both fell in love. During the week of Syaoran's stay, Fei-Wang placed a seal of death on Sakura, and Syaoran decided to stay in Clow to search for a way to stop the curse. As years went on, and the curse was about to activate, Syaoran made a wish to Yūko to turn back time, but at the price of losing his freedom to Fei-Wang. Yūko's assistant, Kimihiro Watanuki, was created to replace Syaoran within his original world's history, and Fei-Wang created the clones of Syaoran and Sakura to use as pawns in an alternate Kingdom of Clow.

The group battles Fei-Wang, who reveals that his agenda is to revive Yūko, who was accidentally frozen in time by Clow to keep her from dying. By reviving her using the powers from the two Sakuras, Fei-Wang will accomplish the "impossible" feat of reviving the dead, proving himself Clow's superior. In doing so, the logic of the world will crumble and everything will be destroyed. Both the Syaoran and Sakura clones are reunited by Yūko, who wishes to compensate them for manipulating them. She sends the clones to another world, where both are reborn as normal humans and have a son. Their son is revealed to be the original Syaoran, who would go to the Kingdom of Clow after the Sakura clone foresaw the future, thus creating a time paradox. In order to break the loop of events and save their friends from Fei-Wang, the clones seal themselves in Yūko's shop until the battle against him, and use Clow's magic to reverse the damage he caused to the worlds. The group is able to kill Fei-Wang, and since time begins moving forward, Yūko dies. However, Syaoran is victim to Fei-Wang's last curse and is trapped in a void between time and space; he drags along his clone and Watanuki due to their connection. As both clones fade away because of Fei-Wang's death, Syaoran and Watanuki pay a price to escape from the void. For their freedom, Syaoran must continue traveling throughout dimensions forever, while Watanuki must forever stay in Yūko's shop. The group rests in the Kingdom of Clow where Fai, Kurogane, and Mokona decide to join Syaoran once again, all hoping to find a way to bring back the clones whose souls still exist as two feathers. Before leaving, Syaoran and Sakura confess their love for each other and reveal their true names: Tsubasa. Though he must travel forever, using his clone's feather, Syaoran's journey will always lead him back to Sakura's side.