In a large pot, warm the olive oil over medium heat. Add the onion and ½ teaspoon salt and cook until the onion has softened, about 3-5 minutes, stirring occasionally.
Add the veggies, garlic, and ½ teaspoon salt and cook until the veggies have softened, about 5 minutes, stirring occasionally.
Make a space in the center for the beef. Add the beef, break it up into chunks, then sprinkle on the remaining ½ teaspoon salt. Cook the beef until it is mostly cooked through, mixing it in with the veg and continuing to break it up into small crumbles along the way, about 3-5 minutes.
Add the tomato paste, smoked paprika, cumin, and oregano. Stir it all up and cook for 1-2 minutes, stirring often.
Stir in the water, beans, chipotles, adobo, soy sauce, and sugar. Bring to a boil over high heat, then reduce the heat to medium-low and simmer rapidly for 15 minutes, stirring occasionally.
Serve topped with lots of cheese and any other toppings you want.