Humanity's battle of many years with the kaiju, giant monsters, has finally come to an end. Now that Earth has entered an age of peace, girls with the souls of kaiju have begun to appear, giving them the ability to transform into kaiju. They are known as the Kaiju Girls, and this is the powerful, transient, beautiful, and at times easygoing story of the strange fate these girls bear.

Kaiju Girls Black is set in Soshigaya-okura, a small town that's not as noisy as the city nor as quiet as the suburbs. In this prosaic setting, an ordinary high school girl named Satsuki Hiraga longs to join the heroic Kaiju Girls organization GIRLS. One day, she awakens to mysterious powers, but Satsuki instead finds herself recruited by Commander Black of the villainous organization, "BLACK STARS". What's a Kaiju Girl to do?