Kyoto was a city in Japan. The Ninth Doctor, Rose Tyler and Jack Harkness visited Kyoto in the year 1336 before their unscheduled arrival on the Game Station. The Doctor recalled how they barely got out alive and laughed about it before a transmat beam penetrated the Doctor's TARDIS and transported them to the Game Station. (TV: Bad Wolf)
This adventure involved the Japanese army and a crashed Volsci ship which the Ninth Doctor managed to get off the ground. (COMIC: Return of the Volsci)
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)