Tokyo was the capital of Japan.
In February 1936, a military revolt engineered by the Sakura Kai and launched by the Japanese First Infantry Division in support of the Kodo Ha broke out in Tokyo against the government. Many government officials and civil servants were killed before the revolt was suppressed. The revolt had a huge influence on Japan's policy of expansion and conquest in China in 1937. (PROSE: The Shadow of Weng-Chiang)
In the same year Coldfire Construction put up a reactor in Peking. This was causing a massive los of power in Peking which was spreading towards Kunming, Shanghai, Pyongyang and Tokyo. (TV: Revenge of the Slitheen)
At 8:40AM GMT on a Wednesday in September 2009, Tokyo was among the numerous places across Earth in which RTAs occurred as a result of the 456 compelling every human child to suddenly stop and proclaim their message: "we are coming." (TV: Children of Earth: Day One)
The Tokyo Space Centre was involved, in 2010, in the teleconferencing that took place during the Atraxi crisis. (TV: The Eleventh Hour) Also during 2010, Axos invaded Tokyo after disguising itself as the headquarters of drinks company Goruda. (COMIC: The Golden Ones)
In 2254, Tokyo was among the major cities where bases were set up by the Daleks, intending to turn Earth into a Dalek production planet, in their attempted invasion which was foiled by the Seventh Doctor. (GAME: Dalek Attack)