By killing them, and then being protected by the US and Britain.
Initially, they killed anybody who left and then came back, or anybody who arrived (except a few portugese a year). Then the US rolled up and forced them to open the country. The US was not interested in having a colony, and wasn’t interested in foreigners blocking their exports to Japan. The British reacted similarly, and both propped up Japan and fended off foreigners while Japan modernized and tried to westernize..
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