Kobato decides to become an honest, humble citizen after enduring a bitter experience known as “wisdom work.” He forms a pact with Osanai, his classmate with the same goal, and they plan to enter high school leading quiet lives. But for some reason, inexplicable events and disasters keep happening around them. Will Kobato and Osanai ever manage to live ordinary, peaceful lives?
Kobato and Osanai made a pact to lead a quiet life as regular students upon entering high school. However, soon after, a handbag mysteriously disappears at the school, and Kobato is asked to help solve the case.
Kobato and Osanai are invited to Dojima's house, where he makes them cocoa using his special method. When Osanai leaves, Dojima asks Kobato about his change in personality.
During a class assignment, a vase in the cabinet seemingly breaks by itself, but there's an elaborate plan behind it. However, this mystery is quickly forgotten when Osanai sees the bicycle thief again and plots revenge.
Kobato, along with Kengo, tries to get to the bottom of Sakagami's motives. It seems there is more to the case than initially suspected. However, Kobato's concern for Osanai is also growing.
Kobato finds Osanai crying in the school hallway, but she runs away without telling him what happened. At the student newspaper club, a new mystery involving Berliner Pfannkuchen (jelly doughnuts) awaits him.
Osanai ropes Kobato into her plans for the summer vacation. However, the cake he is supposed to buy for her proves to be irresistible, even for Kobato.
Just before a date with Osanai, Kobato runs into Kengo, who shares some disturbing news and leaves a strange message. Together with Osanai, Kobato tries to solve the mystery. However, shortly after, it appears that Osanai is in great danger.
When Kobato goes to visit Osanai at her home to invite her to eat candied apples, he learns that she has been kidnapped. Just as he leaves the apartment, he receives a mysterious message from Osanai and, with Kengo's help, sets out to find her.
To top off their summer sweets tour around the city, Osanai treats Kobato to a Tropical Parfait as thanks for rescuing her. Along with this delicious treat, Kobato is also served the whole truth about Osanai's kidnapping.
After a long conversation, Osanai and Kobato come to the conclusion that their agreement has failed – and with it, their friendship. From then on, they go their separate ways.
After starting to get involved with Osanai, Itsukaichi investigates a possible string of fires in the city.
Urino begins writing articles predicting the locations of the next suspicious fires.
There will be a change of pace in the school newspaper. Kobato shows an interest in serial fires.
Urino has a plan to catch the arsonist in the act.
Urino's rules spark escalating arson; Hiyori supports him while Osanai gives advice as bonds shift.
Urino and Kobato both arrive at the site of the final fire.
Kobato explains to Osanai how he arrived at his conclusion about the arsonist’s identity.
Kobato remembers his encounter with Osanai when they were in middle school.
Kobato wakes up in the hospital and sees a box of chocolates with a message from Osanai.
In the hospital, Kobato thinks back to the circumstances around Hisaka's car injury in middle school.
Kobato finally manages to see Osanai in the hospital, revealing a sinister and terrifying truth.
Kobato and Osanai finally find out the whole truth and get help from an old acquaintance.
