Sakura will die if she is left without her memories! But Syaoran makes a deal with the dimensional witch and gives up Sakura's memories of him in order to have the ability to search different worlds to locate her memories.
Sakura, Syaoran and Mokona have encountered a new world of lush green vegetation, but are separated from Kurogane and Fay. Sakura has fallen asleep and Mokona faintly detects the presence of Sakura's feather in this new world that seems to be enclosed inside of a giant birdcage. Overhead, Syaoran hears some rustling and goes to investigate, and finds a hostile little boy who apparently will not let him get to "the princess" - but he isn't referring to Princess Sakura. The king is given a report by one of his aides that things are going smoothly for his plan. But another aide interrupts and whispers that something is going wrong near the town's water supply.
Lo and behold, Kurogane and Fay are sitting right in the middle of the town's water supply. A group of the government's guardsmen comes over to question their presence there, and is appalled to learn they came from the sky through the "Birdcage of Light". Apparently only the king is allowed to do this, so things get ugly. But Fay and Kurogane beat everyone up in their usual style.The little boy has brought Syaoran, Sakura and Mokona to Princess Tomoyo, who resides in a secret place in a quaint little village. The little boy tells Tomoyo that the three may be able to save "Laifan". Tomoyo motions for Sakura and Syaoran to take her hands, and then communicates telepathically to them.
Kurogane and Fay have been imprisoned inside birdcages that are magically sealed. Fay says this is the same kind of seal on the birdcage surrounding the country, where those who are inside cannot get out.
Back at the castle, the king needs "the key", which is hinted to be Tomoyo. The aides haven't found her, but the bird Shinobe says she is in the West Village.
Back to Syaoran, Sakura and Mokona, Tomoyo tells them that everyone in the country has a bird that stays with them all their life. Tomoyo's bird was taken by her uncle. She takes out a small bell that was used to call her bird, but rings it to no avail. Tomoyo's uncle is the king and wants to use Tomoyo to put a seal on the country. With a strange new power that her uncle attained, he has been sealing Tomoyo's voice. Tomoyo takes off her ring and gives it to Sakura. Whenever Sakura has this ring, Tomoyo can talk to her. Suddenly, the same person who interrogated Fay and Kurogane at the water supply barges in and tell Tomoyo to run. But everything in the room begins to go black when huge drapes are pulled over the windows from the outside. Black bird-like figures with shining eyes invade the room and kidnap Princess Tomoyo and Mokona!
Everyone in the village is depressed that Tomoyo was taken and they couldn't do anything. It seems only inevitable that an "eternal darkness" will overtake the entire country now that the king has Tomoyo - the last piece to his puzzle for conquest. But Sakura's possession of Tomoyo's ring - that Tomoyo opportunely gave to her as if she knew she'd be taken - sparks hope. The plan now is to return the ring to Tomoyo.
Mokona and Tomoyo are now with Kurogane and Fay in "jail". Mokona says that it sensed Sakura's feather when the king was near.
Syaoran and Sakura are sealed in barrels and sent downstream to infiltrate the castle, along with the little boy, his bird Kokoruri and the guardsmen. (Reminds you of The Hobbit, doesn't it?) Through what can only be described as the ultimate fanservice, Sakura and Syaoran get some hugging, and rolling and tumbling. The group arrives at the castle, but it might already be too late The aides and some guards attempt to stage a coup against the king, but he blasts them all away. He then begins his plan to put the country in darkness.
Water begins to overflow from the castle and destructively flood the entire country. Syaoran, Sakura and the gang just narrowly escape the surging flow. Those from the West Village can see the silhouette of a giant bird emerging from the castle. The king, with an unconscious Tomoyo, rides the bird upward toward the top of the birdcage.
Mokona says the power of Sakura's feather is getting weaker, which prompts Kurogane to cut through the group's cages.
Syaoran's group wants to use the powerful steam emerging from the castle to get to the king. But from the giant bird's stomach come huge monsters that block their way! Though luckily, Kurogane takes care of them with a quick slice. What a reunion!
Sakura gives Syaoran Tomoyo's ring to give to her. The little boy makes a prayer to Tomoyo's bird Laifan. Syaoran is in a barrel and is launched via steam like a bullet toward the giant bird. The bird partially explodes and the many smaller birds that are freed from the blast catch Syaoran's fall. But the giant bird is now a flying head and continues to soar upward.
But Tomoyo's bell falls toward the ground and rings. Laifan, a giant white bird, emerges and flies Syaoran upward as well.
Tomoyo is being used to blanket the country in darkness, but the action stops prematurily because she doesn't have her ring.
A "battle of the birds" ensues. But Tomoyo tells Syaoran to use the power of her ring. Syaoran kicks and breaks the hat of the king, revealing Sakura's feather, and the ring breaks.
Mokona has opened up a communication with Yuko, who gives the group a key to fix the darkness in exchange for Tomoyo's bell. With the key, the land is restored.
At the end, Laifan, Kokoruri and a number of other birds all fly away. The little boy's name is revealed to be "Koruri". He accepts that he has to let them go.
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