Japan was an island nation off the coast of east Asia. The capital city was Tokyo.
History
Early history
The Ninth Doctor, Rose Tyler and Jack Harkness visited Kyoto, Japan in 1336. (TV: Bad Wolf)
The Eleventh Doctor and Rory Williams briefly visited medieval Japan. (COMIC: The Doctor and the Nurse)
The Seventh Doctor and Chris Cwej visited Japan in 1560. (PROSE: The Room With No Doors)
The Master had the TARDIS take the Eighth Doctor and Izzy Sinclair to Japan in the early 17th century, during an isolationist period, to witness the chaos being caused by the alien "Gaijin". (COMIC: The Road to Hell)
The Doctor witnessed the Earth's fury at the Japanese island of Okushiri in 1720. (PROSE: The English Way of Death)
In 1905, soldiers from the Russo-Japanese War were abducted by the War Lords for use in their war games. (TV: The War Games)
In 1945, two atomic bombs were dropped on Hiroshima and Nagasaki. A third bomb was planned to be dropped on Kyoto, but the aircraft carrying the bomb, the Sky Jack, fell through a black hole. (COMIC: Sky Jacks)
21st century
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. (TV: End of Days)
During the Year That Never Was, the Saxon Master destroyed Japan, watching the islands and its cities and inhabitants burn. However, when the year was erased from history, Japan was returned to its proper place and its people were returned to their homeland. They did not remember their own deaths or anything else that had happened. (TV: Last of the Time Lords) Martha escaped Japan and made her way towards Europe. (PROSE: The Story of Martha)
During the Sontaran invasion of Earth in 2009, Tokyo was the first place of human deaths by the smog which was distributed by ATMOS. (TV: The Poison Sky)
According to Ianto Jones, Japan was one of the first countries where the Daleks landed during their invasion of Earth in the Medusa Cascade. (TV: The Stolen Earth)
Later in 2009, Japan was among the nations which agreed to let John Frobisher speak on their behalf to the 456. (TV: Children of Earth: Day Three)
In the early 21st century, Japan was renowned for its advances in the robotics industry. When Peter Dalton encountered K9, Luke Smith said that K9 was a new robot toy from Japan. (TV: The Wedding of Sarah Jane Smith)
Axos took over Japan through use of ingredients in the Goruda brand drink. The children who had drunk it turned into Axons. (COMIC: The Golden Ones)
Later in the 21st century, Tokyo had a T-Mat centre. (TV: The Seeds of Death)
Due to the destabilisation of the Myloki conflict of 2066-68, Japan invaded New Zealand; by 2096 Tokyo was an independent city-state. (PROSE: The Indestructible Man)
Post-21st century
The Tenth Doctor and Martha Jones travelled to Tokyo in the year 3000, which featured a building known as the Mega Bank of Tokyo. (COMIC: Operation Lock-up)
References
Among the guises employed by Chancellor Goth during his battle with the Fourth Doctor in the Matrix was that of a Japanese samurai. (TV: The Deadly Assassin)
Alternate timeline
During the Year That Never Was, Martha Jones witnessed the islands of Japan go up in flames. (PROSE: The Story of Martha)
