As the head of her middle school's science club, it's only fitting that Ueno is also a brilliant inventor. With devices that can convert any liquid into drinkable water, deodorize the most foul smells, or even generate dark matter to be used as a means of concealment, it seems like nothing is beyond Ueno's capabilities. However, she doesn't invent these devices for the advancement of mankind. Rather, the one force that motivates her is love, the only phenomenon she can't quite figure out. Ueno is head over heels for Tanaka, her nonchalant fellow club member. Yet, because she is too nervous to confess her love and he is too oblivious to notice her affection, her love life is completely stagnant. In Ueno's mind, if she could just expose him to perverted situations, then surely he'd get flustered and fall for her, right? Assisted by her stone-faced classmate and dedicated wingwoman Yamashita, Ueno employs her many inventions on Tanaka in a lewd manner in hopes that he may one day understand how she feels.

In a flooded town where the waters are ever-rising, an old man must constantly build new floors onto his home in order to keep dry. But when his favorite smoking pipe falls into the watery abyss beneath him, he dives into the depths of not only his house, but memories of years past. Tsumiki no Ie is a short film about the everlasting effect of time on one's life—how it can swallow the past entirely, and how one must learn to continue moving forward despite what has already happened.

After the resolution of the debut, Kate and her Doll Emilico have officially become residents of the Shadows House. However, they are under constant vigilance by the Star Bearers—an elite group in charge of the children's wing. In order to escape from their surveillance and the morbid methods they use to keep everyone's loyalty in check, Kate and Emilico must be wary of who to trust and aim to become Star Bearers themselves. Meanwhile, the Star Bearers have encountered their own problems. A mysterious robed figure dubbed Master Robe has trespassed and roams around the children's wing. At first, Master Robe is deemed harmless, but more incidents start occurring that endanger the Dolls' lives—all of them pointing to the suspicious individual. To improve her reputation, Kate decides to solve the mystery herself. Yet, with so few clues and so many suspects, searching for Master Robe and their motive for attacking the mansion proves more challenging than she imagined.

As the season changes from spring to summer, Makoto Yuuki remains alongside the Specialized Extracurricular Execution Squad (SEES). The team continues to defeat Shadows large and small, but they now clash with a new enemy: Strega, a group of rogue Persona users who wish to keep the Dark Hour to their advantage—it seems that Strega may hold a clue to the Dark Hour's true nature. While SEES enjoys summer vacation in Yakushima, they are joined by Aegis, an amnesiac android designed to destroy Shadows. While she proves herself to be a powerful ally, she is inexplicably drawn to Makoto and constantly remains at his side. As they delve deeper into the mysteries of the Dark Hour, the nature of the mysterious connection that binds these two together is slowly unveiled.