The film's story centers on Princess Vanilla, a princess in a land of ice cream, but who nevertheless is unable to create ice cream herself, no matter how much she practices every day. Finally fed up with her lack of ability, she flees her palace, and soon meets Anpanman and Kokin-chan. While traveling with them, she learns the reason why she can't create ice cream. Meanwhile, Baikinman attacks the land of ice cream while Princess Vanilla is missing.

Continuing their journey from Record Country (the place that held the book of memories), Syaoran and company land into Tokyo Country, a blood-filled country under war from opposing factions for natural resources and survival. While reluctantly involved in the race to live, the group faces their own problems as certain revelations are made, changing their journey forever. A shocking betrayal and a battle that risks all of their lives. After this revelation, they will never be the same again.

Based on the novel trilogy of the same name by MAYUMURA Taku (眉村 卓), Time Stranger is the story of a bunch of teenagers getting transported back in time through Japan's history, and getting mixed up with samurai shenanigans.

U.C. 0097, one year after the opening of "Laplace's Box." Despite the revelation of the Universal Century Charter that acknowledges the existence and rights of Newtypes, the framework of the world has not been greatly altered. The conflict later dubbed the "Laplace Incident" is thought to have ended with the downfall of the Neo Zeon remnants known as the Sleeves. In its final battle, two full psycho-frame mobile suits displayed power beyond human understanding. The white unicorn and the black lion were sealed away to remove this danger from people's consciousness, and they should now be completely forgotten. However, the RX-0 Unicorn Gundam 03, which disappeared two years earlier, is now about to show itself in the Earth Sphere once more. A golden phoenix... named Phenex.