In the world of Hidan no Aria AA, there are special students called Butei who are authorized to carry weapons, investigate crimes and solve various incidents. One of the best of these students is an S-rank second year at Tokyo Butei High School named Aria Kanzaki. On the opposite end of the scale is E-rank first year named Akari Mamiya.

The story of the card game follows what happens when "Hairou" portals suddenly open, fusing five different worlds together. As a result, various mysterious "Exceed" powers are awakened in teenaged girls. An academy for these so-called "Progress" girls is built on the isolated Seiran Island in the Pacific.

Mary Bryant, a Cornish girl who was convicted of petty theft, is being transported to the Australian Penal Colony on the First Fleet with other prisoners bound for Botany Bay.