Blue Archive takes place in the academic city-state of Kivotos, which was established by the union of thousands of academies. The citizens of Kivotos are composed of three races: Humanoids, which include subraces ranging from the common human to resembling angels, demons, elves, bioroids, and kemonomimi retaining lesser features of various animal races such as ears and tails; intelligent werebeast citizens of various races; and highly advanced robots with human levels of intelligence and individuality. Due to possessing Halos, humanoids are surprisingly strong and durable enough to resist and survive serious injuries like gunshots and explosions, though they can only be killed by destroying their Halo through certain means. As a result of this, every student possesses some kind of firearm and/or ordnance as a means to protect themselves and fight back against other students, with frequent campus shootouts happening quite a lot across Kivotos.
The city is ruled by the General Student Council (GSC), a federal committee led by a President, who governs the city from the Sanctum Tower with access to every student's register. Despite the GSC having the main authority within Kivotos, many of the schools operate and lead their districts with virtually autonomous independence with almost every school district having a rich, long-lasting history to them, with the three most powerful schools being Millennium Science School, Trinity General School, and Gehenna Academy.
Before the events of the game, the GSC President summons the player character, a teacher with the education status of Sensei, to be the advisor of SCHALE, an extrajudicial organization established by the president herself. She then proceeds to disappear, which is followed by a rise in criminal activity and military presence in the city. As Sensei helps the students, clubs, and academies of Kivotos with their various problems, the Sensei must also deal with school rivalries, criminal warfare, corrupt corporations, rogue AIs, paranormal creatures, mysterious groups, and insidious cults that threaten Kivotos, often with the assistance of their highly advanced smart-tablet known as the "Shittim Chest" and its sentient AI named Arona