Wash and dry the onions, then remove the onion skins and set them aside. Thinly slice the onions.
Heat the olive oil in a large stock pot over medium heat. Add the onions, shiitake stems, and cremini mushrooms and cook, stirring occasionally, for 10 minutes, or until the onions are soft and browned.
Add the water, onion skins, garlic bulb, ginger, dried mushrooms, tamari, and peppercorns. Bring to a boil over high heat, reduce the heat to low, and add the kombu. Cover and simmer for 1 hour. Strain and season to taste.