Preheat and prep the squash: Heat the oven to 400°F (200°C).
Carefully halve the spaghetti squash lengthwise and scoop out the seeds. Drizzle the cut sides with olive oil and season with 1/2 teaspoon salt and 1/4 teaspoon pepper.
Roast: Place the squash cut side down on a parchment-lined sheet pan. Roast for 35–45 minutes, or until the skin gives when pressed and the strands pull apart easily with a fork.
Set aside to cool slightly.
Sauté the aromatics: While the squash roasts, heat 1 tablespoon olive oil in a large skillet over medium. Add the onion and cook 3–4 minutes until translucent. Stir in the garlic and cook 30 seconds until fragrant.
Brown the turkey: Add ground turkey, breaking it up with a spoon.
Season with 1/2 teaspoon salt, 1/4 teaspoon pepper, Italian seasoning, and red pepper flakes if using. Cook until no pink remains and any moisture cooks off, about 6–8 minutes.
Add the sauce: Pour in the marinara and simmer 3–5 minutes to thicken slightly. Taste and adjust seasoning.
You want a well-seasoned, slightly thick sauce.
Shred the squash: Use a fork to scrape the squash into long strands. Transfer to a bowl and gently press with paper towels or a clean kitchen towel to remove excess moisture. Don’t skip this or your casserole may turn watery.
Mix the cheesy layer: In a small bowl, stir together the cottage cheese (or ricotta), 1/2 cup mozzarella, and 2 tablespoons Parmesan. Season with a pinch of salt and pepper.
Assemble: Lightly spray a 9x13-inch baking dish.
Spread half the squash strands in an even layer. Top with half the turkey marinara. Dollop and gently spread half the cheesy mixture.
Repeat with remaining squash, sauce, and cheese mixture.
Add the topping: Sprinkle the remaining 1 cup mozzarella and remaining Parmesan over the top. For extra golden color, lightly mist with olive oil.
Bake: Reduce oven to 375°F (190°C). Bake uncovered for 20–25 minutes, until bubbly around the edges and the cheese is melted and lightly browned.
If needed, broil 1–2 minutes to brown the top more—watch closely.
Rest and serve: Let the casserole rest 10 minutes to set. Garnish with chopped parsley or basil. Slice or scoop and serve warm.