At the stroke of midnight, the Dark Hour appears—a secret hour which most are unaware of. Those not trapped in coffins during this time, unfortunate enough to find themselves conscious, are met by dangerous creatures known as Shadows. A select few, however, possess the potential to wield Persona: a special power used to defeat these beings. This secret group is called SEES (Specialized Extracurricular Execution Squad), and their mission is to uncover the reason behind the Dark Hour's appearance. Only a short while after transfer student Makoto Yuuki begins his residency at Iwatodai Dorm, his Persona awakens after an attack by a strong Shadow. Now recruited into the ranks of SEES, he begins fighting alongside his comrades, as only they can protect humanity from Shadows and prevent the anomaly that is the Dark Hour.

Red panda Retsuko continues to work at her cyclic office job, with the occasional stress-venting via death metal karaoke on the side. With the company of her newfound friends Gori and Washimi, life is more enjoyable than ever before. But some new shake-ups to her status quo threaten to add more stress to her life. At the office, new employee Anai seems like a fine addition to the company. Yet when Retsuko is placed in charge of his training, she finds that beneath his steadfast dedication, he may pose a threat to the stability of the workplace. Meanwhile, at home, Retsuko's mother pays an abrupt visit, fully intent on having her daughter finally settle down and find a man. With this in mind, she sets Retsuko up for various marriage appointments, much to her chagrin. Now, Retsuko finds all the more reasons to head to the karaoke bar and unleash her furious diatribes. However, knowing that this will not truly solve her problems, she decides to make a more spontaneous choice to avoid her issues. And so, Retsuko finds herself set upon another self-reflecting journey, coming to learn more about herself and love, with the ever cathartic support of death metal karaoke.

In the city of Kouchi, high school student Taku Morisaki is going about his work when his friend Yutaka Matsuno calls and asks him to get to their school as soon as possible. Taku arrives, and Matsuno introduces him to Rikako Muto, a beautiful girl from Tokyo who recently transferred to their school. Although Rikako is academically and athletically gifted, her generally unpleasant attitude leaves her with virtually no friends outside of Matsuno and another girl from her class. After a chance encounter during their class trip, Taku suddenly finds himself more involved in Rikako's personal life, much to Matsuno's dismay. Struggling to balance his friendship with Matsuno and his own budding infatuation for Rikako, Taku must come to terms with his feelings and understand how a girl with a troubled past is having such a massive effect on his life.

This musical film is the visual realization of Discovery, an album by Daft Punk. It tells the story of a band of four extraterrestrial musicians who are kidnapped and brought back to Earth by an evil manager. Their only hopes lie with a space pilot from their home planet who, after receiving a distress call broadcasted during the abduction, seeks out to rescue them.