Spirits have always been attracted to Keitarou Gentouga due to his strong spiritual presence. A traumatic encounter with one had caused his right hand to be cursed, forcing him to wear a glove at all times. Now a college freshman, Keitarou is trying to live as normal a life as possible. With the encouragement of his childhood friend Eiko Houzuki, he becomes a private tutor. Since he is at the top of his intake class, his first client is the tutoring firm's most promising student, Yayoi Houzuki. To Keitarou's surprise, Yayoi is Eiko's cousin, and she possesses two pupils in each eye—allowing her to see into the spirit world and purposely seek vengeful spirits to exorcise. Ever since a car accident killed both her parents, Yayoi has been searching for the powerful spirit that kidnapped her mother's departed soul. Seeing that spirits are so attracted to Keitarou, she ropes him into helping her collect other evil spirits that will assist in her future fight. Although her quest is dangerous, Keitarou reluctantly decides to join her, even as each new spirit they meet has him questioning his resolve at every turn.

The Persona Century Corporation has purchased nearly every parcel of land on earth. Dissension is not tolerated within the corporation's borders and those who oppose Persona are dealt with swiftly. Of those few places not yet under Persona's control is the free town of Kabuki-cho, also known as The Dark Side of Tokyo. Within the town, under the leadership of a woman named Mai, is a small resistance group called Messiah. Into this world steps a man who takes the sobriquet of Kabuki-cho: Darkside. Sealed up in another dimension eighteen years ago by Persona Century, Darkside now returns to aid Messiah using his unique mystic power of renewal. (Source: ANN)

Makoto Naegi, a teenager with no remarkable talent, is surprised to learn that he has been accepted into Hope's Peak Private Academy: an elite school that gathers the best students from various fields. Despite believing his admission was just a fluke, Naegi is delighted to attend an institution known for ensuring success to those who graduate. Determined, he enters the front doors of the prestigious academy. However, after losing consciousness inside, Naegi wakes up in a seemingly abandoned classroom. Failing to comprehend how he got there, Naegi begins to explore, and to his surprise, finds his classmates assembled in the gym. While everyone is trying to figure out what happened, they are confronted by the school principal—Monokuma, a robotic teddy bear. The mysterious toy explains that the freshmen are trapped inside the school with only one means of escape—kill a classmate without being discovered. Tension fills the air as Naegi and his classmates realize that they are faced with two choices: participate in Monokuma's killing game, or reside together in the school for the rest of their lives.

On the day of the Tanabata festival, Shidou Itsuka happens to meet the eerie Kurumi Tokisaki, who proceeds to ask him out on a date. Although nervous, Shidou accepts the offer. The two spend their time visiting to a planetarium, buying food at the festival, and trying out a mock wedding ceremony. Meanwhile, Shirou's friends—Tooka Yatogami, Yoshino, and Kotori Itsuka—are looking for him, while also enjoying the festival themselves. As Shidou spends the day with Kurumi, he begins to notice an unexpected softer side of her. He knows that Kurumi is infamously called the Worst Spirit, but the girl standing before him is a gentle soul. However, as the day draws to a close, Shirou finally begins to understand the truth behind it all.