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- At a younger age, Shintaro visited the school cultural festival of Takane's school and met her at a booth that she and her classmate, Haruka, made for the guests. He challenged her to a shooting game fight that she offered to the visitors. Knowing that Takane was known as the second best player in the country, he started to tell her that he's not impressed by her skills. Irritated by the cheeky little boy, she accepted his offer to play and decided to challenge him on the highest level. Before playing the two made a promise that the loser will listen to the winners words while Takane even promised to become his servant and call him her "Master". Eventually Shintaro won the match, but decided to forget about the deal since he saw it as a bother.
- In middle school and high school, he performed as the top of his class in National Mock Examinations. Although he had high academics, his high intellect also caused him to have a very apathetic personality. The only person he finally started to grow to was his classmate Ayano, whom he treated coldly, but who would give him back nothing but friendliness. During high school, he came to reject contact with people after the death of Ayano, shutting himself up in his room. Since then, he started living as a hikikomori, in contact with only the digital world on the internet through his computer, and not the real world. Subsequently, a mysterious software entered his computer, which was sent to him by an unknown person, called "Ene". Being unable to control her actions, his lifestyle was at a loss. Although she told him, "If you keep yourself locked up, you'll always be alone," he always turned a deaf ear to her.
- The "bad route" features Shintaro, shown in a black outfit (referred to as "black Shintaro"). Instead of meeting the Mekakushi Dan, Shintaro remains at home, grieving over the loss of Ayano. He often has visualizations of Ayano, which turn out to be Kano using his eye ability to appear as her, as he believes that Shintaro is the one that caused the death of his precious elder sister. Despite Ene's pleas, Shintaro refuses to go out, eventually gets fed up with her and murders her. After this, Shintaro falls into greater despair, and commits suicide by slitting his throat with a pair of scissors. He later encounters Ayano in the Heat Haze, but is unsuccessful in reaching her unlike Route 1.
Shintaro, in his room, works on a song as his computer freezes, causing him to freak out. As a siren goes off from his computer, Ene appears to ask him if he is alright. As he wonders if he could delete her, she starts renaming his folders and threatens delete the song he just had written. Taking her words as serious, Shintaro starts to panic and spills his soda over his keyboard, causing it to break. As he tells Ene to search for a site to buy a new computer, she explains that it's the Obon festival, held on the 15th August and that no websites will deliver until the following days. Not able to wait that long, the two decide to go out to buy a new computer in a store.
- Outside Shintaro remembers that the city used to look different, but now has changed a lot while he had been at home for two years. They eventually find the building they're looking for while Ene sees an amusement park that she wants to go to. Shintaro declines her wish and reminds her that she doesn't have a body to visit those. The cyber girl gets mad and decides to not talk to Shintaro anymore. She then leaves his phone.
- After entering the mall Shintaro bumps into a clerk, causing him to get nervous about meeting new people again. As he continues his way he then also bumps into Kido, who he apologizes to several times. After she is gone, Shintaro is asked by Ene if he is alright. Just as he responses that he was, he notices an explosion going off and suddenly finds himself in the middle of a group of terrorists.