As spring transitions to summer, Makoto Yuuki maintains their membership in the Specialized Extracurricular Execution Squad (SEES), which continues to successfully defeat Shadows of varying sizes. However, SEES faces a new adversary known as Strega - a group of rogue Persona users who intend to exploit the Dark Hour. Strega's knowledge of the Dark Hour's true nature could prove to be important. During SEES' summer hiatus in Yakushima, they are joined by Aegis, an android with amnesia who was designed to eliminate Shadows. Although Aegis proves to be an invaluable asset to the team, she inexplicably gravitates towards Makoto and remains by his side at all times. As SEES carries on exploring the mysteries surrounding the Dark Hour, the inexplicable connection between Makoto and Aegis begins to unravel.