Prepare the squash: Preheat your oven to 400°F (200°C). Carefully cut each spaghetti squash in half lengthwise and scoop out the seeds. Brush the cut sides with 1 tablespoon of olive oil and season with salt and pepper.
Roast the squash: Place the squash halves cut-side down on a baking sheet lined with parchment paper. Bake for 35-45 minutes, or until the flesh is tender and can be easily scraped with a fork.
Prepare the sauce: While the squash is roasting, heat the remaining 2 tablespoons of olive oil in a large skillet over medium heat. Add the diced onion and cook for 4-5 minutes until softened and translucent.
Add aromatics: Stir in the minced garlic and red pepper flakes, cooking for about 30 seconds until fragrant, being careful not to burn the garlic.
Develop the sauce: Add crushed tomatoes, tomato paste, dried oregano, basil, salt, and pepper to the skillet. Bring to a simmer, then reduce heat to medium-low and cook for 10-15 minutes, stirring occasionally, until the sauce thickens slightly.
Fluff the squash: When the squash is done, flip them over (careful—they’re hot!) and use a fork to gently scrape the insides, creating spaghetti-like strands. Leave the strands in the squash shells, forming a bowl.
Assemble the dish: Spoon the spicy tomato sauce evenly over each squash half, then sprinkle with ¾ cup of the parmesan cheese, dividing it equally among the four halves.
Broil to finish: Switch your oven to broil. Place the filled squash halves under the broiler for 2-3 minutes, just until the cheese melts and begins to bubble and brown slightly.
Garnish and serve: Remove from the oven, sprinkle with remaining parmesan cheese and fresh parsley. Serve immediately while hot.