Three years after the previous game, new protagonist and student teacher Amagi Yuu suddenly finds himself at risk of failing university due to Mature, the school's ice queen of a secretary. Thankfully, he has friends he can rely on, like his classmates Shizuku and Fio, his sister Hotaru, his childhood friend Kisarah, as well as Kagura, whose family shrine is the subject of his school report, and Blue Mary, a mysterious woman he just met.

July 1st to 31st, thirty-one days... will this summer change his entire life?