- Ayano Tateyama: Shintaro first met Ayano in school, and she eventually made contact with him despite his tendency to keep his distance from others. They eventually became close friends. He caught her crying alone in a class room one day, but didn't know what to do, so he walked away. When news spread that she committed suicide during his first high school year, he fell into depression, thinking that she would still be alive if he had talked to her the day before. Then, Shintaro decided to escape and isolate himself from reality to the digital world. Shintaro continuously meets Ayano in the Daze, through his dreams or the start and end of each route, although he doesn't seem to remember these encounters until his ability completely manifests within him. In the anime, it is shown that Ayano was able to speak to Shintaro through her snake. They meet in the Daze to find Haruka. It is hinted that Shintaro has Romantic feelings towards her at the end of the series.
- Takane "Ene" Enomoto: Shintaro was very surprised when he received Ene in a mail from an unknown sender and couldn't delete her anymore, because she had got her own will. He used to really dislike her for her mischief and jokes but has come to rely on and trust her as shown in his faith in her during the terrorist incident. In Route 01, Ene's antics forces Shintaro to leave his house in search of new computer components. This outing results in his first encounter with the Mekakushi Dan. In Route XX, Shintaro becomes fed up with Ene and kills her through unknown means. Shintaro's first meeting with Takane at her cultural festival ended in his thrashing her at her own game, much to Takane's displeasure. The two would continuously butt heads with one another throughout the remainder of their school life, until she became Ene and he shut himself up in his room.
- Momo Kisaragi: Shintaro is Momo's elder brother and although he may not seem like it, he does care for her well-being and health dearly. She shares a lot of character traits with her brother.According to Shintaro, Momo cried a lot when she was small. However, because Shintaro felt like he didn't have the strength to become a good older brother, he could only support her from behind. In the anthology "Christmas Wish", Shintaro asks Kano and Seto to take care of Momo because he lacks the strength to protect someone dear to him. In this case, he is referring to Ayano.
- Marry Kozakura: When the Mekakushi Dan went to the park, Shintaro accompanied her in the ice maze. When she collapsed, Shintaro was forced to carry her back. In the anime, Marry made a pact with him so that he would keep remembering the events that happened to them through his dreams.
- Haruka Kokonose : Before he died and was trapped in the Heat Haze, Haruka (along with Takane) used to spend time with Shintaro and Ayano. But Shintaro, having an apathetic view on life, seemingly didn't pay him much attention. Shintaro, along with Ayano, came to get Haruka from the Heat Haze at the end of the anime.
- Konoha: Konoha and Shintaro seem to be growing pretty close as friends, often spending time together. They even went as far as saving each others' lives. In the anime, Shintaro agreed to help Konoha look for Hiyori and Hibiya, only to see Konoha swallowed by a snake as he tries to save the children.