Taking place after the events of Sakura Wars 2: Thou Shalt Not Die, Sakura Wars 3 follows protagonist Ichiro Ogami join the newly formed Paris Combat Revue and train the "Flower Division", an all-female unit dedicated to fighting supernatural threats against the city while working as a cabaret act. Alongside Ogami's training, the Paris Division must prevent Salu and the Paris Phantoms, the game's main antagonists, from threatening Paris.