Soak beans in a large bowl over-night, covering with about 2 inches of cold water.
In the morning, drain soaked beans and place in a large pot. Cover with several inches of water and bring just to a boil, then immediately reduce heat to somewhere between medium and medium-low or whatever level maintains a gentle simmer. Cook beans for 50-60 minutes, or until beans are tender (but not mushy). Taste test to be sure they are tender before you stop cooking. Drain beans and rinse under cold water to stop the cooking process.
Preheat oven to 275F. Start 1 1/2 cups water to boil.
In a large oven-safe casserole dish with a lid (or alternately, to be covered with aluminum foil), scatter 1/2 of the onion and 1/2 of the bacon over the bottom of the dish. Add 1/2 of the cooked beans. Scatter the remaining onion and bacon, then top with the remaining cooked beans.
In a 4-cup measuring cup or similar sized bowl, stir together the sauce ingredients well. Add 1 1/2 cups of boiling water and stir. Pour over beans and mix gently with a fork. If necessary, add a bit more hot water so that the liquid just barely covers the beans. Cover the pot with a lid or doubled up aluminum foil and place in preheated 275F oven.
Beans will cook in the oven for a total of 6 hours, but should be checked at intervals to ensure there is enough liquid in the pot.
Cook beans for 4 hours, then remove from oven and gently stir with a fork. There should still be enough liquid in the pot to just barely cover the beans, but if not, add more as needed.
Return pot to the oven, covered, checking beans every 30 minutes for the last 2 hours of cooking, first stirring, then adding a bit more water to the pot, if needed. You want to have some puddles of liquid showing on the top of the beans, but you don't want to add too much water to the pot.
After 6 hours of cooking, remove from oven and stir gently with a fork. Let stand, uncovered for 5 minutes or covered for 10-15 minutes before serving.
Notes
Leftover baked beans can be refrigerated for 3-4 days. Fully cooked baked beans can also be frozen for 2-3 months.Be sure to read the notes and see the step-by-step photos above the recipe card for more tips to make this recipe.