Nagisa Aoi is a new transfer student into one of the three prestigious all-girls Catholic high schools on Astraea Hill: a school called St. Miator (the other two are St. Spica and St. Lelim (known in the anime as Le Rim, for some reason). While getting totally lost on her first day, she stumbles into a clearing with a tree, and also into a girl with long silver hair. Nagisa is immediately smitten with the girl, Shizuma Hanazono, otherwise known as the Etoile of the three schools (the most idolized girl). Shizuma, after picking up a figurine dropped by Nagisa, kisses her on the forehead, leading to Nagisa fainting. After waking up in the school's infirmary, Nagisa then meets her new roommate, Tamao Suzumi. Things, however, will be getting a lot more complicated for the new student than just that.

No matter where she goes, Sora takes her sketchbook along. The world is full of mysterious and beautiful things, after all, and Sora doesn't want to miss a single one. The best way she knows to capture each moment is by drawing and sketching, watching and learning.

After the incidents involving Heath Oslo, the existence of the Japanese-American counter-terrorist organization, known as CIRS, is now public knowledge. CIRS was rebuilt from the ground up and its more hidden functions were transferred to a new agency: SORD (Social Ops, Research & Development). The main purpose of SORD is to train a new generation of spies to defend the country from future threats. To achieve its ends, the organization has built many schools in the country. Mihama Academy, abandoned after its sudden closure, has become a specialized training school. So, this new Mihama Academy is home to different groups of students who every day work hard to improve their skills. These students put their own safety at risk by immersing themselves in various extrajudicial missions, all for the good of the country.