Tokyo

Tokyo was the capital of Japan.

History
In 2008, a Samurai warrior was brought forward to the early 21st century by the Rift Manipulator where he began to terrorise travellers on the Tokyo subway system (TW: End of Days)

In the Year That Never Was, Japan (most likely including Tokyo) was destroyed by the Master. This was undone when Jack Harkness destroyed the paradox machine. (DW: Last of the Time Lords)

During the Sontaran invasion of Earth in 2009, Tokyo was the first place of human deaths by the smog which was distributed by ATMOS. (DW: The Poison Sky)

In 2010, Axos invaded Tokyo after disguising itself as the headquarters of drinks company, Goruda. (DWM: The Golden Ones)

Tokyo became an independent state in 2096. (PDA: The Indestructible Man)

The Doctor and Martha traveled to future Tokyo in the year 3000, which featured a building known as the Mega Bank of Tokyo. (DWBIT: Operation Lock-up)