Heat 2 tablespoons oil in a skillet over medium-low heat. Cook pasilla chiles until light brown, being careful not to burn them, 5 to 7 minutes. Transfer chiles to a plate. Increase skillet heat to medium-high; cook tortillas in the same oil until crisp and golden brown, about 3 minutes. Remove from skillet.
Heat the skillet again over medium-high heat. Add tomato and serrano peppers. Roast, turning occasionally, until skin is charred and flesh is soft, 8 to 12 minutes. Let cool briefly. Peel tomatoes and place in a blender along with serrano peppers. Add water and blend until smooth.
Heat remaining 1 tablespoon oil in a saucepan over medium heat. Add onion; cook and stir until translucent, about 5 minutes. Pour in the tomato mixture; cook until thickened, about 5 minutes.
Pour beans into the blender; process until smooth. Add to the saucepan with the tomato mixture. Add oregano and season with salt. Bring soup to a simmer until beans are heated through, about 5 minutes. Garnish soup with the toasted pasilla chile, tortilla strips, and Cotija cheese.