Plot summary

The movie starts with SEES' battle in a full moon phase on July. Junpei Iori, Akihiko Sanada, and Mitsuru Kirijo are fighting the Shadow Arcana Hierophant with Fuuka Yamagishi providing tactical support for them. Meanwhile Makoto Yuki and Yukari Takeba are captured by the Shadow Arcana Lovers and under its spell but eventually free themselves from it. Defeating the Hierophant, Junpei, Akihiko, and Mitsuru regroup with Makoto and Yukari, and they defeat the Arcana Lovers. Unbeknownst to them, they are observed by three mysterious people. Makoto and the others goes to Yakushima for a break and they spend most of the day playing at the beach. While trying to flirt with women under Junpei's insistence, Makoto encounters a mysterious blonde haired girl. At night, Mitsuru's father, Takeharu Kirijo, gathers everyone and reveals that the Dark Hour and the Shadows were created by an accident caused by Mitsuru's grandfather Kouetsu Kirijo and Yukari's father Eiichiro Takeba in an attempt to create a device that could manipulate time. He shows a video left by Yukari's father, who reveals that SEES can end the Dark Hour by destroying the twelve Arcana Shadows. This revelation shocks Yukari who feels responsible for her father's sin, but Makoto comforts her. Entering the Dark Hour, Makoto and Yukari are attacked by Shadows and are almost killed until the blonde haired girl from earlier, revealed to be a Persona user, saved them. Shuji Ikutsuki introduces the girl as Aigis, a 7th Generation Anti-Shadow Suppression Weapon developed by the Kirijo Group, and she joins SEES.Back at the dorm, Mitsuru orders Makoto to pick up Ken Amada, an elementary school student who has the potential to become a Persona user. Moving to the dorm, Ken decides to take a walk, unaware that the Dark Hour has begun. At a nearby shrine, Koromaru, the dog of the deceased shrine owner, is attacked by a Shadow. Makoto arrives and saves Ken before he is devoured by the Shadows. Another Shadow appears, that Ken notices bears resemblance with the one that killed his mother, and he concludes that the Shadows are the ones responsible for his mother's death. Ken swears to annihilate all Shadows and awakens his Persona ability. He and Koromaru, who also has the potential to become a Persona user, join SEES. Entering the full moon phase, SEES prepares to fight another Shadow Arcana. They are approached by Takaya Sakaki and Jin Shirato, who introduce themselves as Strega and reveal that they have come to stop them from eliminating the Dark Hour. They trap them and ask if they truly want the Dark Hour to end. The combined Arcana Chariot and Justice appear and attack. Aigis momentarily gains the advantage by using her Orgia Mode, but quickly overheats, and the rest of the group is weakened by poison gas left by Takaya. Shinjiro Aragaki rescues them by destroying the gate to the area, allowing the poison to disperse, and Makoto destroys the two Shadow Arcanas.At the end of their summer vacation, SEES goes to a summer festival, where Ken bonds with Shinjiro. Entering a new semester, Aigis transfers to Makoto's class. Makoto, Aigis, Yukari, Junpei, and Fuuka share their thoughts about what they will do after the Dark Hour ends. Makoto starts to become afraid that he will lose the meaning of his life if the Dark Hour disappears. This causes Makoto to become hesitant in fighting the Arcana Hermit, frustrating Shinjiro, who loses control of his Persona. Ken recognizes Shinjiro's berserk Persona as the one that killed his mother, realizing that Shinjiro is responsible for his mother's death. On October 4, Ken and Shinjiro are not present for the mission against the Arcana Fortune and Strength. Remembering that October 4 is the date of Ken's mother's death, Akihiko and Mitsuru reveal that two years ago before leaving SEES, Shinjiro's Persona went out of control and accidentally killed Ken's mother. Akihiko attempts to reach Ken and Shinjiro and defuse the situation, but is stopped by the Arcana Fortune and Strength.While Makoto and the others are fighting against the Shadow Arcanas, Ken declares that he will kill Shinjiro, but they are interrupted by Takaya, who reveals the Persona Suppressants that Shinjiro has been taking have been slowly killing him, making Ken's revenge pointless. With Akihiko's help, Makoto eventually defeats the two Shadow Arcanas and hurries to where Ken and Shinjiro is. Ken, losing his will to live, lets Takaya shoot him, but Shinjiro sacrifices himself and takes the bullet instead. By the time Makoto and the others arrive, Shinjiro's wounds are already too severe and he orders Ken to keep on living before dying. On October 7, Shinjiro's funeral is held at Gekkoukan High, and only Akihiko is absent throughout the funeral.After the ending credits, Ryoji Mochizuki is seen standing at the Moonlight Bridge.