From Tardis Wiki, the free Doctor Who reference

Kyoto (meaning "capital city") was a city in Japan. It was formerly known as Heian-kyō.

Japan's imperial court was established in the city 794, when it was known as Heian-kyō. It was renamed to Kyoto three centuries later. (PROSE: The Time Travellers' Almanac)

During the 14th century, the rule of the Kamakura shogunate was ended with the restoration of Emperor Go-Daigo, but this was short lived. In 1336, civil war forced the Emperor to flee to Yoshino, and Kyoto was captured by the Ashikaga shogunate, beginning the Muromachi period of Japanese history. (PROSE: The Time Travellers' Almanac) The Ninth Doctor, Rose Tyler and Jack Harkness visited Kyoto in the year 1336 before their unscheduled arrival on the Game Station. (TV: Bad Wolf) This adventure involved the Japanese army and a crashed Volsci ship which the Doctor managed to get off the ground. (COMIC: Return of the Volsci) The Doctor recalled how they barely got out alive and how they had laughed about it before a transmat beam penetrated the Doctor's TARDIS and transported them to the Game Station. (TV: Bad Wolf)

A third atomic bomb was to be delivered over Kyoto at the end of the Second World War, but the plane delivering it, the Sky Jack, fell through a black hole. (COMIC: Sky Jacks)