Takashi Natsume and his spirit companion Madara, nicknamed "Nyanko," continue returning the names of spirits from the Book of Friends given by his late grandmother Reiko Natsume.

On his way back from school one day, Takashi encounters a lurking spirit named Monmonbou, who recalls memories of Takashi's grandmother after hearing his name. Takashi's natural curiosity leads him to explore a mysterious town where his grandmother used to live. Befriending her old acquaintance Yorie Tsumura and Yorie's son Mukuo, Takashi unveils more of his grandmother's past.

In the meantime, Nyanko detours for food and stumbles upon a suspicious "Spirit Seed," which miraculously sprouts into a fruit tree overnight. Giving in to temptation, Nyanko consumes the fruit, splitting him into three. Seeking a solution to Nyanko's predicament, Takashi and his friends lend a hand, unexpectedly uncovering more secrets the town holds in the process.

[Written by MAL Rewrite]

The film will be made up of two stories: "Ishi Okoshi" and "Ayashiki Raihousha." In "Ishi Okoshi," Natsume meets a small youkai called Mitsumi in a forest. Mitsumi is entrusted to wake up the divine youkai "Iwatetsu" from its deep slumber. Mitsumi weighs on Natsume's mind, so he sets out to help Mitsumi with his task. In "Ayashiki Raihousha," a mysterious visitor appears in front of Tanuma. Nearly every day, the visitor visits Tanuma, talks to him a little, and then leaves. Natsume, who knows the visitor is a youkai, worries for Tanuma, but Tanuma enjoys these exchanges with the youkai. The youkai means no harm, but Tanuma's health slowly starts to deteriorate. (Source: ANN)

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. [Written by MAL Rewrite]

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. [Written by MAL Rewrite]