Preheat your oven to 425°F and lightly grease a large baking sheet. Place the halved spaghetti squash cut-side down on the sheet, then brush the skin with olive oil and season with salt and pepper. Roast for 40 minutes until the flesh is tender and easily pierces with a fork. Once cooked, let cool for a few minutes, then use a fork to scrape the flesh into spaghetti-like strands, being careful not to break through the skin since you'll use the squash halves as serving vessels.
While the squash finishes roasting, melt the butter in a large skillet over medium heat. Add the diced shallot and cook for 3 minutes, stirring occasionally, until softened and fragrant. Add the minced garlic and cook for another minute until it becomes aromatic but not browned. Pour in the heavy cream and mustard, then add the garlic powder, nutmeg, and cayenne. Simmer gently for 5 minutes, stirring occasionally, until the sauce thickens slightly. I like to use quality butter here because it creates a noticeably richer, more luxurious sauce that really elevates the dish.
Reduce the heat to low and stir the Parmesan into the cream sauce from Step 2 until melted and smooth. Add the chopped spinach, basil, lemon zest, and adjust seasoning with the remaining salt and pepper. Cook for about 5 minutes, stirring gently, until the spinach is fully wilted and the sauce is creamy and cohesive. Freshly grated nutmeg really makes a difference in a delicate cream sauce like this—it adds an earthy warmth you can actually taste.
Arrange the roasted squash halves in a 9x13 inch baking dish or similar size. Divide the shredded cooked chicken evenly among the squash halves, then top each with the spinach and cream sauce from Step 3. Sprinkle the mozzarella cheese generously over each portion, ensuring even coverage. Bake at 425°F for 15 minutes until the cheese is melted and the tops are lightly golden. The residual heat from the squash helps everything meld together beautifully.
Remove the baked squash from the oven and let it rest for 2-3 minutes. Top each portion with a sprinkle of fresh Parmesan, additional basil if desired, and red pepper flakes for a subtle heat and color contrast. Serve immediately while the cheese is still hot and melted.