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Once the beans are drained, place them in a large pot. Use a stainless steel, enameled, or other non-reactive pot because reactive materials may alter the taste and color of the natto. Pour enough water into the pot to completely cover the beans. Place the pot on the stove, and bring it to a boil over high heat. Once it's boiling, turn the heat down to medium and allow the beans to simmer for 9 hours. When the soybeans are finished cooking, place a colander or strainer in the sink. Pour the beans into the colander and shake well to remove all of the excess water.
Transfer the beans to a large pot. Cover the beans with water and cook them until they're soft. Strain the beans.