Bring a large pot of salted water to a boil and cook the rigatoni al dente according to package instructions. Save ½ cup of pasta water.
Heat olive in large pan over medium heat and add onion, cooking for 5 minutes or until translucent. Add the garlic, cooking for another 1 minute.
Add the San Marzano tomatoes, tomato paste, crushed red pepper flakes and fennel seeds. Bring to low simmer and simmer for 20 minutes. Stir in the basil and then taste, adjusting for seasoning.
Add the pasta to the sauce along with ¼ cup of water. Stir to combine until pasta is coated. Serve and top with some cheese and more basil if desired.
Notes
You control the amount of heat, so if you like it spicier, increase the crushed red pepper flakes by ¼ teaspoon until you like the spice level. If you want it less spicy reduce the amount by ¼ teaspoon at a time.
Make sure the water you are cooking the pasta in is salted as some of the flavor comes from it.
DO NOT overcook the pasta when boiling. You want it just al dente or slightly under. It continues to cook with the sauce.