The Alphabet Project is a top secret weapons development program sponsored by "Tokyo" in hopes of elevating Japan on the international stage to compete with the United States and Soviet Union. The Alphabet Project is responsible for establishing the Irie Clinic as a research facility dedicated to Hinamizawa Syndrome and its use as a potential weapon. The program was named after their weapon subdivisions: — Atomic (A), Biological (B) and Chemical (C).
Upon the insistence of Koizumi, the Alphabet Project develops an interest in the terminal stages of the Hinamizawa Syndrome, in which one turns paranoid of their surroundings and dies by clawing out their own throat. It seeks to develop a substance which can induce these symptoms voluntarily in a healthy human being as this can prove to be a powerful bacteriological weapon. Miyo Takano, who is the chief authority on the Hinamizawa Syndrome is introduced to the members of the project council and she explains its potential to them in order to garner their interest and further her grandfather's research.
The Alphabet Project agrees to fund the research into the Hinamizawa Syndrome but require a male researcher to be the chief as they do not wish to entrust the responsibility to a woman. Miyo agrees albeit begrudgingly and at her recommendation, Kyousuke Irie is appointed as the chief of the research and the Irie Institution is established under the guise of a local clinic for the village residents. The researchers make significant progress in just a few years as they manage to identify the pathogen, detect the presence of a Queen carrier and develop a proxy vaccine that can suppress the terminal stage symptoms to a great extent with just one injection. Coincidentally, they also discover a substance that can induce the terminal L5 symptoms in a healthy person, which Jirou Tomitake later claims was destroyed.
After the death of Koizumi, who was a major political influence on "Tokyo"'s sponsorship, the Alphabet Project abruptly orders the cessation of this research within three years, citing the UN Biological Weapons Treaty. Miyo's fervent efforts to convince the authorities on the importance of this research fail miserably and she is thoroughly humiliated by those present. She is ultimately ordered to finish any remaining research and develop a working cure within three years after which the Irie Institution will be disbanded and all evidence pertaining to the research will be destroyed. This threat to her research will drive Miyo to join forces with Nomura and plot to destroy Hinamizawa as a desperate attempt to validate her grandfather's theories.