Having attended Mihama Academy for about a year, Yuuji Kazami has seemingly found his place within the school, but he suddenly decides to pursue a promotion in CIRS. After consulting JB about his intentions, they both thoroughly examine Yuuji's documents and dissect the events of his upbringing to determine if the job is fit for him.

Meanwhile, unbeknownst to the two, the girls of Mihama uncover some torn documents in Yuuji's room. After restoring the papers, they discover the story that has formed—or perhaps broken—Yuuji into the man he is today. However, what was thought to be history has haunted him to the present, and the chains of the past begin to drag him back into the darkness...