Some history
Tokyo's rise to importance can be largely attributed to two men: Tokugawa Ieyasu and Emperor Meiji. In 1603, after unifying the warring states of Japan, Shogun Tokugawa Ieyasu made Edo (now Tokyo) his base. As a result, the city developed rapidly and grew to become one of the largest cities in the world with a population topping one million by the 18th century. It became the de facto capital of Japan 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 figurehead 17-year-old Emperor Meiji moved to Edo, which was renamed "Tokyo" ("Eastern Capital") the year before. Tokyo was already the nation's political, economic, and cultural center, 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.
Tokyo, like Osaka, has been designed since about the turn of the century (1900) to be rail-centric, that is centered around major train stations in a high density fashion, so suburban railways were built relatively cheaply at street level. This differs from other world cities such as Los Angeles that are low density automobile centric, and though expressways have been built, the basic design hasn't changed to this day.
Tokyo's subway and commuter rail network became the busiest in the world as more and more people moved to the area. In the 1980s, real estate prices skyrocketed during an economic bubble. The bubble burst in the early 1990s and many companies, banks, and individuals were caught with real estate shrinking in value. A major recession followed, making the 1990s Japan's "lost decade" from which it is now slowly recovering.
Tokyo was hit by powerful earthquakes in 1703, 1782, 1812, 1855 and 1923. The 1923 earthquake, with an estimated magnitude of 8.3, killed 142,000 people.