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This is not a time period I am very good with, and I apologize if my question has an obvious answer. I come to learn.
Could the Allies have just blockaded Japan until they surrendered? Just sink any ships they have left... eventually they will run out of critical resources due to the lack of said key resources on the Japanese islands.
This came from a debate against a friend really into WWII... and this idea occured to me.
(I am sorry to say that my fool of a friend thinks unmentionable seamammal would have worked...)