Preheat oven to 400 degrees.
Put squash in a microwave safe bowl with 1/2 C water, cover in plastic wrap leaving a small hole for steam, and microwave until the squash starts to become tender, about 5 minutes. Drain and set aside.
Melt 2 Tbsp butter in ovenproof large frying pan or cast iron skillet. Add the onion and thyme and cook, stirring, until the onion softens and becomes translucent, about 5 minutes. Add the squash, garlic, nutmeg, cinnamon, salt and pepper and cook about 1 minute until garlic is fragrant. Add the broth and simmer until at least half the broth has been absorbed. Stir in the heavy cream and bring to a simmer again, cooking about 2 minutes until slightly thickened. Remove from heat. (At this point the squash should be able to be pierced with a fork but not be totally fork tender yet).
Melt the remaining 1 Tbsp butter in the microwave and toss with the bread crumbs parmesan, parsley and a pinch of salt and pepper. Sprinkle over the squash and then top with the shredded gruyere. Transfer skillet to the oven and bake until bubbly and golden, about 30 minutes. Let rest 5 minutes before serving.
Enjoy!