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Heat oven to 375 degrees F. Coat a 9x13-inch casserole dish with cooking spray and set aside. Steam squash until very soft, about 20 minutes, then puree in a food processor and set aside.
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At the same time, cook pasta according to package directions until very al dente. (It will finish cooking in the oven.) Drain and set aside.
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For the sauce: Melt butter in a medium pot over medium-high heat. Add flour and stir constantly until lightly browned, 2-3 minutes. Slowly add warm milk, whisking continuously until smooth. Bring to a boil, then reduce to a simmer and cook, stirring frequently, until thickened, 5-7 minutes. Add squash puree, salt, pepper, gruyere, mascarpone, and thyme and stir until smooth.
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For the topping: In a small bowl, combine bread crumbs, olive oil, garlic, and Parmesan.
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Mix cooked pasta with the butternut squash cheese sauce and pour into prepared casserole dish. Sprinkle with breadcrumb mixture. Bake 30-35 minutes until bubbling and golden brown.