Pierce the spaghetti squash in a few spots with a sharp knife. Microwave 5 minutes; turn to the other side and microwave 5 more minutes, until soft to the touch. Let stand for 5 minutes to finish cooking.
Using a sharp knife, cut the spaghetti squash in half lengthwise. Allow it to cool for 5 minutes, until easier to handle. Scoop out the pulp and seeds from the center, then rake a fork back and forth to remove strands of the flesh onto a serving bowl. Set aside.
Cook the sauce:
Heat the oil in a large, deep saucepan over medium-high heat, about 3 minutes. Add the beef, onions, salt and pepper. Sauté, breaking up the beef as you cook, until beef is no longer raw, about 5 minutes.
Stir in the marinara sauce. Bring to a boil, then lower heat to medium-low and simmer, covered, stirring occasionally, 20 minutes.
Finish the dish:
Ladle the meat sauce over the squash noodles, top with parsley and Parmesan, and serve.
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Notes
Cooking spaghetti squash in the microwave can result in mushier results than roasting it in the oven. To minimize mushiness, it's important not to overcook the squash. If it does end up overcooked, simply place the squash halves, cut side down, on a clean towel for a few minutes. This will help absorb some of the liquid.