Drain and rinse 1 can black beans and 1 can kidney beans. (Do not drain the third can.)
Saute onion in hot oil in a large Dutch oven over medium-high heat 5 to 6 minutes or until tender.
Add garlic and saute another 1 to 2 minutes.
Stir in chili powder, ground cumin, red pepper flakes, pepper, and salt; saute for 2 to 3 minutes.
Stir in diced tomatoes, drained and undrained beans, and 2 cups vegetable stock.
Bring to a boil over medium-high heat; reduce heat to medium-low, and simmer, for 30 minutes, stirring occasionally.
Season with salt and pepper to taste.
Serve chili with desired toppings.