As a child, Kotarou once won a race event using his rewrite ability. This caused him to be ostracized in class and attract unwanted trouble, so he decided to do badly during the next test, eliminating other people's suspicion towards him. Because his power caused him to become unnaturally stronger, he could not enjoy any sports activity.
During his middle school years, Kotarou was being dragged by his parents, who worked for Martel, to attend their meetings. However, Kotarou hated what they were discussing, and since he wasn't allowed to speak his mind about said meetings without being scolded, he grew distant from his family.
At night, Kotarou would hunt UMAs, but one night he went into the forest and encountered a dinosaur-like familiar. The familiar proved to be too powerful for him, then the Bayern Knights appeared and defeated the familiar. There he met their leader Esaka.
Kotarou is occassionally asked by Iko Fuku, a caretaker of a local orphanage, to look after a young Akane Senri. Around that time, Kotarou also met a young Kotori Kanbe, who had a bad impression of him after seeing him pick a fight on the street in order to help a young Haruhiko Yoshino get his money back.
She was also brought by her parents to attend to Martel's meeting at one time, but was able to convince them not to make her attend. In exchange, Kotori was tasked to take care of Pero, a dog who was abused by his previous owner. At one time, Pero escaped and went missing. Kotarou was able to locate him. Pero did not live long after that.
After seeing Kotori's perseverance, Kotarou then decided to stop going to Martel's meetings which resulted in an argument with his parents. He then decided to run away, asking Esaka to let him become a member of their organization, Guardian, and undergo training.
During the training, Kotarou was paired with Arata, Touka, and Nagai, as they were the people who had the lowest scores in the exam training. At first, Kotarou had very little confidence in himself, but it gradually began to grow as he connected with with his other teammates. They all became members by the end, except Nagai, who quit due to her low self-confidence and subsequent loss of powers.
He was sent to Kazamatsuri for an assignment, where he was given the fake identity of Bondo Kazamatsuri (風祭 凡人 Kazamatsuri Bondo), though he found it to be too obvious. He was not allowed to reveal his identity during the stay, as he was declared missing, but he encountered Akane who got lost, so he returned her back to the orphanage. He introduced himself to Iko as Bondo Suzuki (鈴木 凡人 Suzuki Bondo) instead. There he found out that the orphanage provides for children with developmental disabilities.
Their first assignment involved them stationed near an alley inside Kazamatsuri, but Arata and Touka became impatient and headed for the forest instead. Kotarou, concerned, followed them as well. In the forest he witnessed Mikuni, another Guardian, meeting his demise in a fight against the Earth Dragon.
Kotarou fled from the scene and found tiny footprints that lead him to Akane who was stuck at the top of a tree. He managed to get her down while being attacked by a hound familiar, but as he tried to escape her, he came across a newborn Key. But he left the scene and went back to Guardian HQ then makes lie for the report.
In Kotarou's second year of high school, feeling that he has been wasting time not achieving anything. He spent his time poking fun at Yoshino and accompanying Kotori. Time by time Kotori's mother asks him to look for her daughter, in which he would know that she is somewhere in the forest.
He then begins to experience strange phenomena, namely a strange presence around him and a "ghost" haunting him in his room at night.
At Kazamatsuri Academy where he studies, he continues to spend time with Kotori and Yoshino. During lunch time, he found a student outside the school building stuck on a tree and helped her, but he ended up seeing her underwear. This was caused by the heavy box she was carrying, which was too heavy for Kotarou but something she can easily lift. Finding it awkward to leave her carrying it, he insisted on helping her, which caused her to fall again. He later finds out that her name is Ohtori. The awkward events in their meeting, plus his allusion to the pattern of her underwear another time he met her, caused her to hate him.
That time, Kotarou was applying for Terra Magazine as a stringer for the Harvest Festival, which he needed a camera. While looking for a camera in the alleyway, he meets a man wearing contemporary clothing.
The next day, he meets the moral guard Shizuru Nakatsu in the hallway, warning him not to run at the hallway. The two occasionally eat together outside the building.
After his first encounter with the Leaf Dragon, Kotarou went back to the school one week later and continue his normal life. Kotarou get into a fight with Yoshino as Yoshino can not tolarate with his action when his homeroom teacher mention that Kotori is going to switch school without any prior reason. After Yoshino gives a good beating, Kotarou suddenly remembers about all the event that happen in the forest.
After the event in the forest, Kotarou went back to the school, only to notice all the girls from the Occult Club went missing, except Chihaya who casually enter the classroom.
Kotarou wakes up on his bed, remembering what happen during the encounter with the Leaf Dragon. When Pani and Gil approach him, he became paranoid and ask them to leave the house. But he realized that there is a time gap between the day in the forest and on the current day. He then called out to Esaka.
Kotarou received a quest to investigate on a certain Haruka Asahi's curse.
Akane sends Kotarou a message telling him to proceed to the clubroom, and though he has a lot of questions for her, she tells him that she will not answer any of them and that he should just go back to his normal life. Kotarou refuses, becoming heartbroken by the fact that the Occult Club and its members will never return to how it was before. Akane consoles Kotarou and decides to admit him into Gaia as her bodyguard.
Kotarou wakes up in his bed, remembering some scene that happen in each of the character route. After that, he travel along the destroyed city and arrive a hill which he meet Kagari. Kotarou tried to communicate with Kagari but being killed by her multiple times. But after awhile, Kotarou manage to get close enough to Kagari and tried to help her.
Kotarou uses his rewrite ability to rewrite his brain to able to understand the project that Kagari is working on but he rewrites too much and pass the point of no return. He then has to be saved by Kagari.
The story progress until the point where Kagari does not know how to proceed with her project. Kotarou decides to help her and manage to create a possibility for the route that Kagari wasn't able to get any future from it.
However, before the project can be completed, they were interrupted by Sakura Kashima. Kotarou then summon all the member of Occult Club in order to protect Kagari from the attack launced by Sakura Kashima.
The story tells Kotarou's past up until the scene of Kagari's birth. Instead of attacking or capturing her, he decides to let her go unharmed. He did not report this to Guardian. Seeing this as an act of betrayal, Kotarou decides to work outside Japan.
He then participated in a war in a foreign land, where he befriended a colleague named Luis.
He went back to being alone, unable to contact his friends from the Occult Club. Shizuru momentarily appeared in school, to bid goodbye to him. He then encounters the "ghost." She introduced herself as Kagari, who have lost her memories except for her name, and is asking him to help her find herself. Kotarou suggested her to find herself in his computer. The next day, they met again in school. The two walked around the campus, where Kagari found fondness over feecof. Going outside, he encountered an amnesiac Inoue, where she gave him a memory card. The contents of the card detailed her experiences in the forest