Rika Furude and her group of friends live in the small mountain village of Hinamizawa; in June 1983, they welcome transfer student Keiichi Maebara into their ranks, making him the only boy in their group. After school, they have fun playing games and spending each day living their lives to the fullest. Despite this seemingly normal routine, Keiichi begins noticing strange behavior from his friends, who seem to be hiding the town's dark secrets from him. Elsewhere, a certain person watches these increasingly unsettling events unfold and remembers all the times that this, and other similar stories, have played out. Using that knowledge, this person decides to fix these broken worlds. However, when certain variables change, the individual is faced with a horrifying realization: they have no idea what to expect or how to stop the impending tragedy.

Es awakens in the facility Milgram to find a strange talking animal named Jackalope staring them down. Soon, they learn their purpose: as the prison guard, Es must delve into the psyches of 10 inmates, each of them imprisoned for causing the loss of life in some form or another. Their fates rest in Es' hands. Do the means justify an end, and how much does intent matter if the result is death? No matter how the lines between good and evil, right and wrong, and just and cruel are blurred, there are only two options Es can choose between: innocent or guilty.

Rika Furude and Satoko Houjou are best friends who have lived in the small village of Hinamizawa for their entire lives. Alongside their other friends, they spend every day together, and every moment is filled with fun and laughter. However, as Rika and Satoko begin to grow older, a life-changing opportunity presents itself to both of them. Rika is determined to follow her dreams and wants Satoko by her side. Although Satoko is hesitant, she decides to walk this path with Rika. However, the realization of her dream forms a rift between them. This leaves the girls living in completely different worlds, with Rika enjoying her new life and making new friends while Satoko grows more and more isolated. Longing to return to the nostalgic days in Hinamizawa, Satoko despairs and wishes things could be changed. Just when she is at wits' end, an encounter with a supernatural entity changes Satoko's perception and imparts new revelations about her best friend Rika. This begins her journey to get the future she desires—by any means necessary.

In 2008, the Japanese government began hunting people who identify as otaku in an effort to protect the country's culture. In just one week, the enforcement agency known as the SSC captured almost every otaku by force and confiscated their memorabilia. One passionate man calling himself Otaku Hero refuses to allow this agency to do as they please: he raises a resistance army made up of other displaced geeks who band together to help defend their culture. Three years later, the fires of rebellion wane as all hope seems lost for otakus. Spurred on by his ally—the magical girl Anarchy—Otaku Hero commands the resistance in an effort to reunite Anarchy with the other two other magical girls: Blue and Pink. By combining the power of this trio, the resistance may be able to defeat the SSC and save otaku culture for everyone.