Preheat your oven to 450℉. Add the butternut squash to a large sheet tray and drizzle with 1 tablespoon olive oil and sprinkle with 1 teaspoon salt and ½ teaspoon pepper. Roast for 20 minutes until tender. Add to a blender or food processor and puree.
Bring a pot of salted water to a boil and cook your pasta according to package directions until al dente. Drain and set aside.
Meanwhile, in a large pot, melt the butter and sauté the garlic, onion, and red pepper flakes for 3-5 minutes. Add in the flour and cook for 1 minute until lightly golden.
Add in the milk, heavy cream, and pureed butternut squash. Bring to a boil then reduce to a simmer and allow to simmer for 5 minutes, stirring occasionally, until slightly thickened.
Add the cheese to the milk/cream mixture and stir to combine. Add in the drained pasta and stir in to finish melting the cheese.
Add the mac & cheese to the baking dish and sprinkle with the panko and chopped sage. Bake for 15-20 minutes until golden brown.