Preheat and prep the squash. Heat the oven to 400°F (200°C). Line a baking sheet with parchment.
Carefully slice the spaghetti squash in half lengthwise and scoop out the seeds.
Season and roast. Rub the cut sides with olive oil, then season with salt, pepper, and half the Italian seasoning. Place cut-side down on the sheet and roast for 35–45 minutes, until the shells yield slightly when pressed and the strands pull apart easily with a fork.
Brown the protein. While the squash roasts, warm a skillet over medium heat. Add the turkey or chicken sausage and cook, breaking it up, until browned and cooked through, 5–7 minutes.
Stir in the garlic and cook 30–60 seconds until fragrant.
Make the sauce mix. Reduce heat to low. Stir in the marinara, remaining Italian seasoning, and a pinch of salt. If using, blend the cottage cheese until smooth, then stir it into the sauce for extra creaminess and protein.
Simmer 2–3 minutes to meld flavors.
Shred the squash. Remove the squash from the oven and flip it cut-side up. Let it cool slightly, then use a fork to loosen the strands, keeping them in the shells to form “boats.”
Combine and stuff. Add half the mozzarella and the Parmesan to the skillet mixture and stir until just combined. Divide the mixture between the two squash boats and toss gently to coat the strands evenly.
Top like pizza. Sprinkle the remaining mozzarella over the boats.
Add turkey pepperoni, olives, and a pinch of red pepper flakes if you like.
Bake until bubbly. Return the stuffed boats to the oven and bake 10–12 minutes, until the cheese is melted and golden in spots. For extra browning, broil 1–2 minutes, watching closely.
Garnish and serve. Let rest 5 minutes. Sprinkle with fresh basil or parsley.
Serve hot, straight from the boats, with a fork and spoon to twirl the strands.