In the spring, male student Makoto Yuki transfers to Gekkoukan High School. However, as he heads to his new dormitory, listening to the music on his headphones, he is stopped. More precisely, time has stopped, and the people who were around him turn into coffins. Makoto learns that this period of time hidden between the minute of midnight is called the Dark Hour, a time when monsters called Shadows appear. Suddenly made the leader of his fellow classmates Yukari and Junpei by his upperclassmen Mitsuru and Akihiko, Makoto must learn empathy, his connection to his comrades, and the meaning of death. With the power of his Evoker aimed at his head he awakens a Persona and fights against the Shadows threatening to attack his world from the mysterious tower of Tartarus.

Makoto Yuki and his allies have grown through the bonds they have formed and partings they have experienced. Using the power of Persona, they continue to fight to put an end to the Dark Hour, in hope that there are peaceful days waiting for them at the end of the battle. However, as the season shifts to winter, memories from ten years ago resurface and a boy believed to be their friend warns the members of S.E.E.S. that "The Fall"— an event that will destroy all of humanity is near, leaving the group with a difficult choice to be made by New Year’s Eve.

The season turns to autumn and the fight of Makoto and his group S.E.E.S. with the strange monsters known as ‘Shadows’ is getting closer to the end. Makoto and his allies engage in life-or-death battles with Shadows in order to end the Dark Hour. Through the battles, some must face the deaths of friends and family, some must notice what precious things must be protected, and some must find meaning in the battles that have occurred. In front of Makoto, the mysterious transfer student Ryoji Mochizuki appears. When the group greets a new morning, the gears of fate begin to turn. A fight revolving around each of the heroes' bonds begins...

A spin-off scenario taking place after the events of the TV special Dragon Ball Z: Bardock - The Father of Goku, in which Bardock survives the destruction of Planet Vegeta and is sent into the past, combating Frieza's ancestor Chilled and turning into a Super Saiyan.

Mother's lucky day takes a strange turn when a lightning strike leaves her with telekinetic powers. She finds more and more ways to use her new ability, but soon things get a little out of control.