Step 1: Sweat (gently cook, no browning) the vegetables until the onions become translucent. Add salt, pepper, red chili flakes, and tomato paste. Stir in and let warm until the tomato paste is starting to caramelize.
Step 4: Once the beans have fully softened, use an immersion blender and puree until the soup is very smooth. (A countertop blender can be used. Let soup cool a bit before blending.)