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The surface of the clinic is normal, appearing as a regular clinic, although it also acts as a hospital. Hōjō Satoko was once hospitalized there for her terminal Hinamizawa Syndrome, and dismissed. The interior of the clinic is furnished well, with paintings and potted plants. It is unknown whether or not this facility contains an X-ray generator above ground, though it is almost certain that it has this and more underground.
The clinic closes at 6:55 PM every day, while the opening time is unknown.
The basement contains an advance security system that includes a near-perfect surveillance system, a counterintrusive gas release system, and a large research lab.Although the surveillance system is supposedly flawless, it did not observe Akasaka's existence and his entering into Rika's household, causing the Yamainu and Takano to face problems in Matsuribayashi-hen. The security system is also able to pick up which member of the clinic's ID is being used to gain access to the underground facility.
The gas counterintrusive measures start once a red emergency button is pressed, alerting the facility of intruders. In 120 seconds a suppressive gas is released, either killing or knocking out the intruders. Staff members are provided with a gas mask, and while the facility is preparing to release the gas all electronically controlled exits are closed. The gas that is used itself is unknown.
The most important part of the underground facility is the research labs, where Irie and his fellow researchers study the Hinamizawa Syndrome. It is well equipped, supposedly possessing an electron microscope of its own. Multiple operating rooms are down in this area as well. It is also within this area that vivisections on terminal patients are carried out.
The facility is accessed via ID cards, with the hospital members and the Yamainu being able to access it.
Within the underground facility also lies a comatose Satoshi. The facility has been in care of him for around a year, therefore it's safe to assume it could also have several other rooms for comatose patients (such as the post-vivisection test subjects).
It is revealed that the clinic is conducting research into the Hinamizawa syndrome. To assist their studies, they ask Furude Rika and Hōjō Satoko if they can use them as research material, since Satoko is one of the only known survivors of Level 5 of the syndrome, and Rika is supposedly the "Queen Carrier", meaning if she were to die, the entirety of the village would hit LV5 within 48 hours. Needless to say, it is in their best interest to keep Rika alive and well. In Matsuribayashi-hen, it is also revealed that Hōjō Satoshi, having over worked himself taking care of his younger sister, developed the syndrome. He was immediately hospitalized and placed in intensive care in the basement. Satoshi is, as of Matsuribayashi-hen and onward, still in the clinic in a medically induced coma. Sonozaki Shion visits him frequently.