The group arrives in a desolated Tokyo. Running under cover from the acid rain, Syaoran and Mokona run into Kamui and his group. Sustaining bad injuries, Syaoran is rescued by Kurogane, who then fights Kamui until to a draw. Deciding that the travelers aren't thieves, Kamui allows the group shelter and receive treatment for Syaoran's wounds. Kurogane speaks to Fai about his past, and then later the group runs into Fūma and his group. The Syaoran being held captive by Fei Wong Reed awakens.

It is revealed that the Syaoran that has been collecting the feathers so far is a clone and that the real Syaoran was the one trapped by Fei Wang Reed. The story continues as the awakened Syaoran travels towards his clone. The seal on the "heart" in the clone's right eye is broken, and Fai tries to restore it with his magic, but fails. Without the heart anymore the clone Syaoran's instincts (reasons why he was created) kick in, making him forget his own developing heart. Fai's left eye is eaten by the clone and battle breaks out between the real Syaoran and the clone. As the real Syaoran is about to strike the Clone, Sakura begs them to stop and because of this, the Clone stabs Syaoran, obtains the feather and gives it to Sakura. The Clone then leaves through a portal opened by his creator, Fei Wong Reed, ignoring Sakura's desperate pleas for him to stay. Later, Subaru, Kamui’s twin, wakes up from his coma.

After the Clone left, the water has drained from the Municipal building and Fai is dying due to the loss of his eye that the clone ate. Subaru wishes to have the water restored, while Kurogane wishes to save Fai's life. Fai is fed with vampire blood and becomes a vampire, thus saving his life, and the water is restored. The price of the water, however, is that Sakura must seek out a treasure somewhere in Tokyo. In the process of searching, Sakura is injured while battling her way out. Her left eye is injured and left arm wrenched out, mirroring the injuries Syaoran had suffered. Later, she is saved on her way back by a mysterious girl (Sakura Kinomoto) and makes it back. The people of Tokyo Tower give their feather to the people of the building in exchange for letting them all live in the building. Yūko reveals that Fei Wong Reed is behind Sakura's lost feathers and their journey across the dimensions, informing them that he needs Sakura to have the memories of many dimensions imprinted upon her body. Sakura decides to find clone Syaoran, together with the others who, for their own personal reasons, start to travel into another dimension again, leaving the last feather behind to ward the water and the building to protect the people of Tokyo.