The story of the movie is somewhat based on the plot of the most recent game, "Sakura Wars 3," released back in March this year. While the game features Lieutenant Ohgami, the main character who takes off for Paris, narrates one side of the story, the movie unveils the secrets behind Hanagumi. Ohgami leaves for Paris, consequently leaving Hanagumi without a leader; thus a new character will be introduced here. To be replaced with Lieutenant Ohgami is the former leader of Hoshigumi, Rachette Artile - a rationalistic and distinct individual, who brings about serious problems to Hanagumi. The members are now in discord with Rachette. Meanwhile, Teikoku Kagekidan was being threatened by some irrelevant demons and a new type of anti-kouma mechas, (brought by an american company) appears and tries to replace the koubu-kai. Having made repeated mistakes due to the absence of Ohgami, Hanagumi is now faced with an unprecedented danger, while the abolishment of Teikoku Kagekidan Hanagumi is being schemed.
为了给妹妹报仇，Heya进入了一所名为Denitix Academy的专门学校，该学校训练战士对抗外星实体。在学院里，学生被分为两类：潘多拉和支配者。就这样，Kazuya遇到了一群身体虚弱但异常强壮的女孩。其中，被称为最强潘多拉的夏蒂莱萨（由奈登美子配音）最让卡祖亚感到担忧。一次偶然的机会，Kazuya出乎意料地与她搭档。此外，还有甘妮莎（Hidamura秀吉配音）和神秘的西藏转学生拉娜·林琴（Huaze Caraway配音）这样骄傲温柔的女性。在战斗和学习的过程中，Kazuya下定决心揭开她姐姐的死亡之谜。
杰森·伯恩事件引发了连锁反应，Treadstone计划和中央情报局利用药物管制加强特工的做法在报纸上公开，导致背后的人坐立不安。为了防止失去一切的情况，中央情报局高层决定暂停该计划，并将相关特工和科学家从行动中清除。
