Combine the first 11 ingredients (through dried pepper flakes) in a large stockpot. Crumble in the ground beef.
Cover the pot and cook over high heat, bringing the mixture to a boil. Uncover and reduce to a simmer. Cook, stirring occasionally, for 45 minutes to an hour, or until the chili is the consistency you want.
While the chili cooks, prepare the rest of your toppings…cook the pasta according to package directions and shred the cheese. Heat the beans in a medium-sized skillet until warmed through. Heat the chopped onions in a small skillet over low heat until softened, about 12-15 minutes.
To assemble: Fill the bottom of your plate or bowl with pasta. Top with chili, followed by cheese. Finish with onions and beans, if eating a 4- or 5-way dish. Enjoy!