Combine the beans, onion, bay leaf and water in a large saucepan. Bring to a boil, then let boil for 1 minute. Lower the heat to medium and simmer, uncovered, for 40 minutes, until the beans are very tender and about half the water has evaporated. Remove the bay leaf and onion before serving.
While the beans are cooking, prepare the chipotle adobo sauce: In a heavy bottomed skillet over medium heat, saute the onion and garlic in the olive oil until the onion is very soft, 10 to 12 minutes. Stir in the chipotles and adobo sauce, cook for 30 seconds, and remove from heat.
Allow to cool a few minutes, empty the sauce into a food processor bowl, and briefly pulse until a chunky sauce forms. You may also use an immersion blender to do this. Serve the sauce drizzled over individual servings of beans.