Sakura Wars 3 takes place following the events of Sakura Wars 2. Series protagonist Ichiro Ogami joins the newly formed Paris Assault Troupe to train their own Flower Division, an all-female unit dedicated to fighting supernatural threats against the city while maintaining their cover as a cabaret act. The Paris Assault Troupe must learn to work together to defend their city against a series of mysterious phantoms seeking vengeance against Paris for their fallen ancient civilization.