Preheat the oven to 375°F (190°C).
Boil the penne pasta in a large pot of salted water for 2 minutes less than the package instructions for al dente texture.
Reserve 1/2 cup of pasta water, then drain the pasta.
In a large mixing bowl, combine the cooked pasta, marinara sauce, minced garlic, olive oil, dried oregano, red pepper flakes, and the reserved pasta water.
Transfer half of the pasta mixture into a 9x13 inch baking dish.
Sprinkle 1 cup of mozzarella cheese over the first layer of pasta.
Add the remaining pasta mixture on top.
Evenly distribute the remaining 1 cup of mozzarella and the 1/2 cup of grated parmesan cheese over the surface.
Bake for 20 to 25 minutes until the cheese is melted, bubbling, and slightly golden on the edges.
Allow to rest for 5 minutes and garnish with fresh basil before serving.