Preheat and prep the squash: Preheat your oven to 400°F (200°C).
Halve the spaghetti squash lengthwise and scoop out the seeds. Drizzle the cut sides with 1 tablespoon olive oil and season with a pinch of salt and pepper. Place cut side down on a parchment-lined baking sheet.
Roast until tender: Bake for 35–45 minutes, depending on size, until the squash is easily pierced with a fork and strands pull away from the skin.
Set aside to cool slightly. Reduce oven temperature to 375°F (190°C) for baking the casserole.
Cook the turkey mixture: While the squash roasts, heat the remaining 1 tablespoon olive oil in a large skillet over medium heat. Add the onion and cook 3–4 minutes until softened.
Stir in the garlic and cook 30 seconds until fragrant.
Brown and season: Add the ground turkey, breaking it up as it cooks. Season with 1 teaspoon salt, 1/2 teaspoon black pepper, Italian seasoning, and crushed red pepper flakes if using. Cook until no longer pink and lightly browned, about 6–8 minutes.
Add marinara: Pour in the marinara sauce and bring to a gentle simmer.
Taste and adjust seasoning. Turn off the heat.
Shred the squash: Use a fork to scrape the roasted squash into strands. Transfer to a large bowl and gently blot with paper towels if it seems watery.
You should have about 5–6 cups of strands.
Combine and add cheese: Add the turkey marinara to the bowl with the squash. Stir in the Parmesan and 1 cup of the mozzarella until evenly coated.
Assemble the bake: Spread the mixture into a lightly greased 9x13-inch baking dish (or similar). Top with the remaining 1/2 cup mozzarella.
Bake to bubbly: Bake at 375°F for 18–22 minutes, until heated through and the cheese is melted and lightly golden in spots.
Rest and serve: Let it rest for 5–10 minutes so it sets up a bit.
Sprinkle with fresh basil or parsley if you like. Serve warm with extra Parmesan.