Heat the olive oil in a large Dutch oven or heavy soup pot over medium-high heat. Add the onion and bell pepper; cook, stirring occasionally, until softened and just starting to color, about 5 minutes.

Add the garlic, chipotle peppers, adobo sauce, cumin, smoked paprika, salt, and black pepper. Cook, stirring constantly, until deeply fragrant, about 2 minutes. This wakes up the spices and tames the raw bite of the chipotle.

Pour in the black beans, fire-roasted tomatoes with their juices, vegetable broth, and the bay leaf. Stir well, scraping up the browned bits from the bottom of the pot. Bring to a lively boil.

Reduce the heat to medium-low and simmer uncovered, stirring occasionally, until the beans are very tender and the flavors have come together, about 15 minutes. Fish out and discard the bay leaf.

Use a potato masher to mash roughly one-third of the beans right in the pot — about 15 firm presses. Stir the mashed beans back in; the soup should thicken noticeably while keeping plenty of whole-bean texture. No roux, no blender, no extra step.

Stir in the lime juice and cilantro. Taste and add more salt if needed — beans are thirsty for salt. Ladle into bowls and serve with Greek yogurt, avocado, cotija, tortilla chips, and extra lime wedges.