O filme segue com o desfecho da série e com a rota da Light Novel. Trinta anos após a falha do Programa de Colonização Espacial. A Humanidade quase foi extinta. Uma eterna e mortal Chuva cai sobre a Terra. Homens conhecidos como “Kuzuya” roubam bens e artefatos das ruínas das civilizações. Um Kuzuya esgueirava-se na mais perigosa de todas as ruínas – a “Cidade Sarcófago”, no centro desta cidade morta, ele descobre um planetário de antes da guerra. E quando ele entra no lugar é saudado por Hoshino Yumemi, um robô companheiro. Sem um único pingo de dúvida, ela assume que ele é seu primeiro cliente nos últimos 30 anos. Ela tenta lhe mostrar as estrelas, mas o projetor esta quebrado. Incapaz de entender o que está acontecendo, ele acaba concordado em concertar o projetor…
Kota Mizutani, a 10-year-old boy whose health worsened after he saw a murder, is brought to Akiko's clinic by his mother Mariko. Kota says that two months ago, he witnessed a man in a park strangling a woman with a cord and was chased by the man afterwards. Hamada, who listens to his story along with Akiko, immediately performs an investigation but cannot find any traces of the crime. However, Kota's testimony gains credence when the body of a woman killed two months before is discovered on a construction site in Kawagoe. Acting on a tip from a citizen who says she had been wearing the same clothes as the victim, the police search the house of Kazuko Shimazaki, a photographer who is often absent. But when Kazuko returns from her trip with her assistant Hirano, it becomes clear the victim is a different person.
An attorney from Yokohama is found murdered at Lake Toya in Hokkaido. Uematsu (Noi Yasuo), of the Hokkaido police goes to Yokohama in search of Konno Shizuka (Watanabe Azusa), a woman who may know something about the case. He tries to take her in to the station for questioning. Muta (Kobayashi Keiju) happens to be there as well. Muta learns that Konno has a debt with a moneylender in Hokkaido.
Tadateru Matsudaira, the sixth son of Ieyasu Tokugawa, was exiled for not taking part in the attack on Osaka Castle. 10 years before his exile expired, he was attacked in a clandestine Yagyu operation believed to have been ordered by his older brother Hidetada. In order to correct his brother's true intentions, Tadateru broke the law and went all the way from Hida Province, where he was exiled, to Edo Castle. However, the Yagyu do not stop trying to kill Tadateru...
Rumors are circulating that the shogunate is losing control of some feudal domains. Lord Yagyu Munefuyu is assigned to deal with the problem and the rebellious clans will be crushed! Meanwhile, a former vassal of the Kazama clan is shot and killed. Moments later a second man is killed by a mysterious master swordsman. Matsudaira Choshichiro and his companions arrive at the crime scene and find a new type of repeating gun. The carved seal on the gun stock belong to the Saiga; a ninja clan abolished by the shogunate many years ago. The blame for the murders is placed on the Kazama clan. Are they guilty or is this a wise cunning plan by Lord Yagyu to be able to destroy the Kazama clan? Choshichiro sets out to reveal the truth and try to save the doomed Kazama clan! In his way are the Owari, Lord Yagyu and his ninja assassins, and the mysterious master swordsman! Will Choshichiro prevail against impossible odds...?
