The transforming assassin Golden Darkness, known as Yami, returns to Rito Yuuki's town to dig into her own origins, and finds her artificial younger sister Mea Kurosaki being steered by the shadowy Nemesis. Tearju Lunatique, the scientist who created both of them, now teaches at Rito's school and wants the three of them to live as the family they never had. Meanwhile Princess Momo Deviluke keeps pushing her Harem Plan to install Rito as king of the Devilukean empire, while his old crush Haruna Sairenji edges closer to admitting her own feelings. This second season continues directly from the previous one.