The story takes place in Sugomori, a city built upon reclaimed land that once prospered as a futuristic city. One high school boy living there, Agata Katsuhira, is somehow unable to feel any pain. One day just before the start of summer break, Katsuhira is called by a mysterious girl named Sonozaki Noriko and chosen to become one of a group of people who share one another's pain: a "Kiznaiver." Several of his classmates have also been chosen as part of this group, but they're all people from different circles who normally wouldn't associate with each other.
Sonozaki calls this an experiment for the purpose of guiding their battle-ridden world toward peace. After learning all this, many trials befall them one after another. The story of the summer experienced by these students chosen to bear one another's pain begins here!