Shintaro is the main protagonist of the series. A digital girl named Ene that lives inside his computer causes him to go outside for the first time in two years, where he meets the Mekakushi Dan and becomes its seventh member.

Shintaro is a young man with an IQ of 168. Thanks to his high intelligence and likely the latent use of his eye ability, Retaining Eyes, he has perfect photographic memory. However, likely due to subconscious memories of past Routes, he finds that everything in the world is predictable and has obvious answers, and he would get perfect scores on his exams and even games he has not played before. Because of this, Shintaro grew up with an apathetic personality. In middle school, he was openly selfish and arrogant and showed signs of depression. It is implied that his loneliness prior to meeting Ayano Tateyama is a significant contributing factor to his depression and also his personality.

During his first year in high school, he became close friends with his upperclassman Haruka Kokonose, and they would spend time with Ayano and Takane Enomoto often. He becomes distraught after learning about Haruka's imminent death by his illness. On the night of August 15th of that year, he meets Ayano, whom he doesn't know is actually Kano using his eye ability. Kano tells him that "everything is your fault". The next day, he learns about Ayano, Haruka and Takane's deaths, and afterwards, devastated, he drops out of school and becomes a NEET. He also does not go outside for two years until the present plot. A year before the present plot, he downloads Ene from an email from an unknown sender and is thereupon unable to remove her from his computer.

Retaining Eyes: Shintaro's eye ability, given to him by Marry after promising long ago to "never forget this Tragedy", allows him to remember everything he sees. Unlike others, he does not visit the Kagerou Daze each Route to gain this ability and instead has it since before birth. When his ability is fully activated, he can remember events of past Routes and directly speak with the Snake of Retaining Eyes. In Manga Route 2, Ayano Tateyama trades her life to become the snake for this ability.