Tokyo

Tokyo was the capital of Japan.

In the Year That Never Was, Japan (most likely including Tokyo) was destroyed by the Master, in his new empire. The damage done by the Master, was undone when Jack Harkness destroyed the paradox machine. (DW: Last of the Time Lords)

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

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)