The story follows Rino Rando, who has been on her own since the passing of her mother, Chieri, as she transfers to Miyagami Private Academy with the recommendation of her mysterious pen pal, Mr. Poppit. Shortly after her arrival, Rino surprisingly becomes a member of elite group of girls called the Best Student Council. Rino learns that Kanade Jinguji founded Miyagami Private Academy as a place where students can live free from restrictions and that the Best Student Council was formed to ensure that freedom. Best Student Council Members receive free tuition, room and board.

The story takes place at Miyagami Private Academy, a mysterious all-girl high school, its student council, the Miyagami Academy Maximum Authority Wielding Best Student Council, also known as the Best Student Council (Gokujou Seitokai), having their own Assault, Covert, and vehicle divisions. This council has more authority power than any of the faculty and staff members. The Best Student Council is divided into the four main divisions: Executive, Assault and Covert plus the Vehicle Squad. Each member of the council has their own special ability, such as special fighting techniques, the gathering of information, or weaponry such as cards, a yo-yo, or, in Rino's case, her hand puppet, Pucchan. It is revealed in an early episode that no one really knows how many members are actually in the best Student Council except the President.