Preheat your oven to 400 degrees.
Coat your prepared spaghetti squash halves with olive oil, and season with salt and pepper. Line a cookie sheet with foil and place the squash cut side down and roast for 35-45 minutes. They are done when the skin starts to brown and soften and you can pierce the skin easily with the tip of a knife.
While the squash is roasting, heat a tablespoon of olive oil in a medium pot and saute the chopped onion until it is tender and translucent, about 10 minutes. Add the red pepper flakes and ground beef. Cook the beef, breaking it up with your spoon, until it is cooked through. Add the marinara sauce and mix well. If you have some red wine open, add about a quarter cup. Simmer the sauce with a lid for about at least 20 minutes or up to an hour on very low heat.
Once your squash is done and cool enough to handle, fluff up the “spaghetti” strands with a fork. Top each half with small spoonfuls of the ricotta cheese. Nestle some of the ricotta cheese into the squash strands. Add a little of the mozzerella and parmesan cheese on top of the ricotta. Spoon about a cup of sauce (or more if it fits) into each half of squash. Reserve any left over sauce for serving or store in the refrigerator for another use. Top with with the remaining mozzarella and parmesan cheeses. Put the filled squash back in the oven for about 15 minutes or until the cheese is melted and bubbly. Top with fresh basil and serve!