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There were two main factors that led to the erosion of the Tokugawa Shogunate and the Meiji Restoration. First, there was the rise of the merchant class and the decline in the power of the samurai that came with it. Second, there was the pressure from the West, epitomized by the "opening" of Japan by Commodore Perry.
As the Tokugawa era came to a close, the merchant class in Japan had become very powerful. They were very rich and the samurai class depended on them for money. This went against the formal hierarchy in which merchants were the lowest rung. This disparity between the formal system and reality eroded the foundations of the Tokugawa government.
Second, the intrusion of the West, in the form of Perry, severely shook the foundations of Japanese society. The country, which had thought itself superior and invulnerable, was badly shocked by the fact that the West was stronger than Japan. This led to political upheaval as various factions pushed for various different solutions to the issue.
Overall, then, Japan's feudal society had been eroding for some time. When Perry "opened" Japan, the structure of Tokugawa government was given a push and its eroded foundations were revealed. This led to the fall of the Tokugawa and the Meiji Restoration.
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