Agata Katsuhira is a strange young man who doesn't feel pain. One day, he encounters a mysterious young woman named Sonozaki Noriko, who changes his life, as well as the lives of his classmates forever.
The kids are forced into doing self introductions... However, it appears that the self introductions that Sonozaki wants them to do requires much more than the usual name and what class they're in. They find out that every wrong answer has a penalty, and painfully learn that they are indeed connected to each other...
The kids find out that there's actually one other Kiznaiver, and they go to find this mysterious figure.
The kids get to know Hisomu and Sonozaki promises to let them know a secret about Kiznaivers if they agree to go to a summer training camp.
The Kiznaivers get to their training camp and are faced with the summer favorite, the test of bravery. Meanwhile, Chidori runs off on her own and the others realize that they might be connected by other means than just their pain.
Something from Honoka's past comes back to haunt her, and Nico makes another attempt at becoming her friend.
The Kiznaivers find out the truth about Maki's past, and try to help her overcome it.
The Kiznaivers get stuck in a building during a typhoon and some hidden feelings start to come to light.
The Kiznaivers start to hear each others thoughts, which makes things even more complicated. Meanwhile, a secret about Sonozaki and Katsuhira is revealed.
The Kiznaivers all go their own ways. Meanwhile, Katsuhira finds out the truth about the Kizna Experiment and about Sonozaki's past.
Katsuhira finds out what happened to the friends from his childhood and Sonozaki is intent on making the Kizna Experiment successful no matter what.
Katsuhira catches up to Sonozaki in order to try to stop her from trying to connect everyone to the Kizna System.