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Tokyo was originally a small fishing village named Edo.

It was first fortified by the Edo clan, in the late 12th century.

In 1457, Ōta Dōkan built Edo Castle. In 1590, Tokugawa Ieyasu made Edo his base and when he became shogun in 1603, the town became the center of his nationwide military government. During the subsequent Edo period, Edo grew into one of the largest cities in the world with a population topping one million by the 18th century.[12]

It became the de facto capital of Japan[13] even while the emperor lived in Kyoto, the imperial capital. After about 263 years, the shogunate was overthrown under the banner of restoring imperial rule. In 1869, the 17-year-old Emperor Meiji moved to Edo. Tokyo was already the nation's political and cultural center,[14] and the emperor's residence made it a de facto imperial capital as well with the former Edo Castle becoming the Imperial Palace. The city of Tokyo was established, and continued to be the capital until it was abolished as a municipality in 1943 and merged with the "Metropolitan Prefecture" of Tokyo.

Central Tokyo, like Osaka, has been designed since about 1900 to be centered around major train stations in a high-density fashion, so suburban railways were built relatively cheaply at street level and with their own right-of-way. This differs from many cities in the United States that are low-density and automobile-centric. Though expressways have been built in Tokyo, the basic design has not changed.

Tokyo went on to suffer two major catastrophes in the 20th century, but it recovered from both. One was the 1923 Great Kantō earthquake, which left 140,000 dead or missing,[15] and the other was World War II. The bombing of Tokyo in 1944 and 1945, with 75,000 to 200,000 killed and half of the city destroyed, was almost as devastating as the atomic bombs of Hiroshima and Nagasaki combined.[16]

After the war, Tokyo was completely rebuilt, and was showcased to the world during the 1964 Summer Olympics. The 1970s brought new high-rise developments such as Sunshine 60, a new and controversial[17] airport at Narita in 1978 (some distance outside city limits), and a population increase to about 11 million (in the metropolitan area).

Tokyo's subway and commuter rail network became one of the busiest in the world[18] as more and more people moved to the area. In the 1980s, real estate prices skyrocketed during a real estate and debt bubble. The bubble burst in the early 1990s, and many companies, banks, and individuals were caught with mortgage backed debts while real estate was shrinking in value. A major recession followed, making the 1990s Japan's "lost decade"[19] from which it is now slowly recovering.

Tokyo still sees new urban developments on large lots of less profitable land. Recent projects include Ebisu Garden Place, Tennozu Isle, Shiodome, Roppongi Hills, Shinagawa (now also a Shinkansen station), and the Marunouchi side of Tokyo Station. Buildings of significance are demolished for more up-to-date shopping facilities such as Omotesando Hills.

Land reclamation projects in Tokyo have also been going on for centuries. The most prominent is the Odaiba area, now a major shopping and entertainment center. Various plans have been proposed[20] for transferring national government functions from Tokyo to secondary capitals in other regions of Japan, in order to slow down rapid development in Tokyo and revitalize economically lagging areas of the country. These plans have been controversial[21] within Japan and have yet to be realized.