Shibuya 109 Shelter (渋谷のシェルター１０９) is located at Shibuya and is the main location as well as the largest shelter where most survivors in Tokyo live. There are currently 55 survivors living beneath it. According to Denjirou Shiba's notes, these group of people are the only survivors left in Tokyo after Ibara and her group rescued the others previously in the first and second arc. The one who created and made this place was Denjirou. It has the theme from the Taisho era recreation (大正).
Since most of the area has become an ocean-like city, they have to board onto the Hovercraft to be able to reach the shelter. Akiko explains that "Shibuya is on lower ground than surrounding areas. So the water gradually pooled up over the past 20 years".
Akiko further explains that "It was built to be a nuclear shelter. Dr.Shiba designed it at the government's request...at the same time they were building Daiba Nuclear Power Plant. The higherups were supposed to use this shelter if anything ever went wrong at the plant. But the meltdown was far more serious than anything they ever expected. In the end, the government chose to give up on the capital, and left via helicopters..abandoning most of its citizens."
The "Four-leaf Clover House" was the first building built in this shelter. It is now where Akiko, Ryuunosuke and Alice lives. Other buildings and facilities are added later by Dr.Shiba and the survivors after they have settled and live here.