Preheat your oven to 300°F / 150°C.
In a large, heavy-bottomed, oven-safe pot or Dutch oven, heat the oil over medium-high heat.
Add the chopped onions and cook, stirring often, until soft and golden, about 7-8 minutes.
Stir in the tomato paste and cook for another minute until it darkens in color, which deepens its flavor.
Pour in 6 cups (1440 ml) of water, scraping up any delicious browned bits from the bottom of the pot.
Add the kombu, soaked beans, molasses, and dry mustard.
Stir everything together to combine.
Cover the pot and transfer it to the preheated oven.
Bake for 2 hours, leaving it completely undisturbed.
Carefully remove the pot from the oven and give it a stir.
Check the liquid level; if the beans aren't submerged, add a little more hot water.
Cover and return to the oven to cook until the beans are completely tender, which can take another 30 minutes to 2 hours depending on the age and type of your beans.
Once tender, season with salt and pepper and stir well. This helps the kombu break down and dissolve into the sauce.
Taste and adjust with more molasses or mustard if desired.
Increase the oven temperature to 400°F / 200°C. Return the pot to the oven, uncovered, and bake for about 30 more minutes, or until the sauce has thickened and the beans are beautifully creamy.
Let them rest for a few minutes before serving.