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Step 1
Drain beans of soaking water, and combine in a heavy soup pot or casserole with 2 of the fresh bay leaves, the whole onions, salt and water to cover by a depth of 2 or 3 fingers. Bring slowly to a boil over medium heat. Meanwhile, keep a tea-kettle of hot water handy to add as the water in the pot is absorbed by the beans. You want to keep them mostly under water. Reduce heat, place on a flame tamer if desired, and simmer until beans are tender, stirring occasionally, about 1-1/2 to 2 hours or longer, depending on freshness of beans. Test by removing a bean and slicing through it crosswise.
Step 2
When beans are tender, remove whole onion(s) and bay leaves.
Step 3
Make a sofrito from the aromatics: in a large heavy saute pan, swirl some olive oil over medium high heat until hot and shimmering. Add diced onion and the 3 bay leaves and saute until onion is golden and translucent. Push aside some onion, add a bit of olive oil, and add the garlic. Saute until fragrant, and toss with the onions. Add the minced chipotle chili, stir for a few seconds, remove from heat, then stir in the ground chili, cumin, and oregano. Add the 1/2 teaspoon of salt and stir again.
Step 4
Add sofrito to the pot of beans, then stir in the canned tomatoes with some juice, squeezing tomatoes in your hand to break them up before dropping them in the pot. With a soup ladle, remove about 3/4 of a cup of the broth to a small bowl or coffee cup and add the tablespoon of unsweetened cocoa powder. Whisk until smooth. Add back to the pot. Taste for salt and seasoning, adding more to taste if necessary, and simmer over low heat another 30 minutes or so until flavors are blended and tomatoes are broken down. Can be prepared up to this point one day before, chilled and reheated just before serving--this will develop the flavor further.
Step 5
Serve chili with brown rice, onions, cheddar and/or goat cheese, yogurt, lime quarters guacamole and salsa for everyone to layer as they like.
Step 6
Halve the avocados and squeeze out of their shells. Mash coarsely with a fork.
Step 7
Stir in garlic and lime juice. Serve as an accompaniment to chili.