Roast the spaghetti squash according to these instructions, or cook the spaghetti squash using your preferred method.

Prepare the mushroom bolognese sauce. In a large saute pan or pot, heat the olive oil over medium and add the chopped onion. Saute, stirring frequently, until onion his very fragrant and has softened, about 8 minutes.

Add the chopped mushrooms and garlic, and saute, stirring occasionally, until very fragrant, about 3 to 5 minutes. Add the garlic, rosemary, oregano, paprika, red pepper flakes, and sea salt and cook another 2 minutes.

Add the crushed tomatoes and bring sauce to a gentle boil. Reduce the heat to a simmer, cover, and cook 30 minutes (or longer to maximize flavor if desired).

Remove the cover and cook at a gentle boil for 10 minutes, until sauce is thick. Add the chopped basil, stir, and set sauce aside until ready to use.

Preheat the oven to 400 degrees F and lightly spray or oil a small casserole dish (9-inch square or round will work great!).

Transfer the cooked spaghetti squash to the prepared casserole dish and sprinkle with sea salt. Pour the mushroom bolognese sauce over the spaghetti squash noodles, then top with the grated mozzarella, parmesan, and ricotta cheeses.

Bake on the center rack of the preheated oven for 30 to 45 minutes, until cheese is golden brown and sauce is bubbling.

Remove from oven and allow casserole to sit 30 minutes before serving.