Short answers, pulled from the story.
Tokyo Bay is located in the southern Kanto region of Japan, spanning the coasts of Tokyo, Kanagawa Prefecture, and Chiba Prefecture on the southern coast of Honshu. It connects to the Pacific Ocean via the Uraga Channel.
In the narrow sense, Tokyo Bay covers about 922 square kilometers. Including the Uraga Channel, the broader area reaches approximately 1,100 square kilometers, and the combined total with the channel is 1,500 square kilometers.
Sarushima, a 0.055 square kilometer island off Yokosuka in Kanagawa Prefecture, is the only natural island in Tokyo Bay. It served as a fortification site during the Bakumatsu and Meiji periods and is now an uninhabited marine park.
Commodore Matthew Perry sailed his four Black Ships into Edo Bay on the 8th of July, 1853, to pressure the Tokugawa shogunate into opening Japan to American trade. The negotiations he began led to a peace and trade treaty between the United States and Japan in 1854.
The Japanese Instrument of Surrender was signed on the 2nd of September, 1945, aboard a warship anchored in Tokyo Bay at coordinates 35 degrees 21 minutes 17 seconds north, 139 degrees 45 minutes 36 seconds east. A flag from one of Commodore Perry's original ships was displayed at the ceremony.
Tokyo Bay contained about 249 square kilometers of reclaimed land as of 2012. Land reclamation has been ongoing since the Meiji period, using sand dredged from the bay floor, and continues to gradually reduce the bay's area.