There are generally two accepted core rationales for why Japan became much more restricted during the Sakoku policy era (it should be noted that Japan was not entirely closed off, but incredibly heavily restricted in terms of where and who could trade). It should be noted that the Sakoku policy (enforced in 1639 formally) was instigated after an uprising that threatened an only relatively won peace.

Just to provide a brief timeline of events leading up to Sakoku:

• 1467 - The Omin War over shogunate succession becomes the first of a long series of conflicts
• 1467 - 1600 - A continuous string of warlords and local lords wage combat in an attempt to become the final victor, with no one side ever able to completely claim dominance
• 1600 - The Battle of Sekigahara ends the major conflicts in favor of the Tokugawa loyalists
• 1603 - The Tokugawa Shogunate is formally established, creating a new national governmental ruler
• 1615 - The Siege of Osaka marks the last conflict between the lingering loyalists to a rival lord and Tokugawa's forces, cementing the Tokugawa Shogunate's rule

One theory is that it was a reaction to the increasing influence that foreign powers were having on Japan, both economically and religiously. A large number of traders were also accompanied by missionaries coming to spread Christianity, an entirely new mindset and religious belief to Japan (at least in any significant force). Because Christianity, especially in the middle ages, tended to want to have loyalty to the church first and all others second, this was contrary to the ruling policies of the Tokugawa shogunate who ran the country at the time. There was also fear of becoming more economically entwined and dependent on other nations, which was considered a potential threat to the peace and stability that had been hard earned after decades of conflict during the Sengoku period.

A second theory is that this was all to further secure the Tokugawa's power and influence over the nation. As stated, the country had just gone through a massive series of conflicts and war during the Sengoku period before stability was established with the Tokugawa shogunate. Individual lords (called Daimyo) were able to use the trade and cultural influences (primarily the Spanish and Portuguese) to gain their own powerbases and military might, which could create a potential threat to the recently established order. By restricting trade and cultural exchange, they were able to ensure that there would be minimal threats to their power structure, since no foreign power could provide an excess amount of aid to an individual lord.

What triggered the event was known as the Simbara Rebellion, where a large group of converted Catholic peasants began to revolt after a mix of feeling religiously persecuted and overtaxed due to construction of a new castle. When the revolt settled, the government accused missionaries of fostering the feelings of rebellion and kicked most of them out of the country, and heavily restricted what foreigners could do. Trade with countries like Spain and Portugal were almost entirely cut off, while trade was still lightly conducted with the English and Dutch, since they were less directly related to entwine religion with their trade practices, though their trade was also heavily restricted to one or two very isolated ports with heavy government restrictions.