Start by cooking your penne pasta according to the package instructions, but reduce the cooking time by 2 minutes. You want it to be slightly undercooked as it will continue to cook in the oven. Drain and set aside.
In a large skillet, heat 3 tablespoons of olive oil over medium heat. Add the chopped onion and cook until translucent, about 5 minutes. Stir in the chopped garlic and cook for an additional minute, until fragrant.
Add the drained and chopped tomatoes to the skillet, followed by the dried basil, crushed red pepper flakes, and salt. Pour in the chicken broth, stirring to combine. Let the sauce simmer for about 10 minutes, allowing the flavors to meld together.
In a large mixing bowl, combine the cooked penne pasta with the tomato sauce, mixing until well coated. Gently stir in the shredded Havarti cheese and black olives.
Preheat your oven to 375°F (190°C). Transfer the pasta mixture into a greased baking dish. Sprinkle the grated Parmesan cheese evenly over the top.
Bake in the preheated oven for 25-30 minutes, or until the cheese is bubbly and golden brown.
Once out of the oven, let the dish cool for a few minutes. Garnish with freshly chopped basil for a pop of color and added flavor before serving.