Poke holes with a fork in the skin of the butternut squash halves, Place squash, garlic cloves, and shallots on a foil-lined baking sheet.
Roast about 25 minutes, until the shallots and garlic are lightly golden brown and tender. Remove them, and continue to roast the squash another 20-30 minutes until it is fork tender. After it's baked, allow to cool 10 minutes before attempting to handle.
Remove seeds and guts of squash, then spoon roasted squash, shallots, and garlic into food processor and puree until mostly smooth. Set aside.
Brown Butter Breadcrumbs
While squash is roasting, melt butter over medium heat in a small saucepan. Cook, swirling the pan occasionally, and watching for it to turn a golden brown color and begin to release a nutty smell. Add breadcrumbs to butter over the breadcrumbs and stir with a fork, then set aside.
Combine ricotta, egg, sage, salt and pepper in a small bowl and stir until well combined. Refrigerate until ready to assemble.
Place the butter in a skillet over medium heat. Once melted and hot, add in the sage leaves and cook for 1-2 minutes, flipping halfway through. Remove and drain them on a paper towel.
Butternut Squash Cheese Sauce
Preheat oven to 375 degrees F. Spray a 9x13 casserole dish with cooking spray and set aside.
Bring a large saucepan of water to a boil. Salt the water, then add the pasta and cook, stirring occasionally, until al dente. Drain and rinse pasta and transfer to a large bowl.
Melt butter in a medium saucepan over medium-high heat. Add the flour and whisk, stirring well, and cook about 1 minute until slightly browned. Whisk in the milk, cream, nutmeg and salt and pepper. Simmer for about 5 minutes, whisking often to prevent scorching, until mixture begins to bubble up.
Remove from the heat and whisk in the Gruyère and white cheddar, stirring until smooth. Add the pureed butternut squash and stir until well combined.
Reserve 1¾ cup sauce in a measuring cup, then pour remaining sauce into the pasta bowl and toss to combine.
Spread 1 cup sauce in the bottom of the prepared casserole dish. Pour in ½ of the pasta. Spread ricotta mixture on top. Add remaining pasta and the rest of the cheese sauce. Sprinkle top with shredded Fontina and Parmesan, brown butter breadcrumbs, and fried sage leaves.
Tent with foil and bake 15-25 minutes, until the cheese is melted. Remove foil and broil on high for 4 minutes. Let stand about 5 minutes before serving. Enjoy!