Preheat oven to 400℉. Cut squash in half length wise and scoop out all seeds. Brush the olive oil on the flesh of the squash and sprinkle with salt and pepper. Spray a baking sheet with oil or line with parchment paper and place the squash onto the baking sheet. Bake for 40-50 minutes, until fork tender. When the squash is finished roasting, reduce oven heat to 350℉.
Bring a large pot of salted water to a boil and cook macaroni al dente, according to package instructions. Drain and set aside.
In a small mixing bowl, combine the crushed ritz crackers, onion powder, garlic powder, and melted butter. Stir to combine. (this will be a crumbly mixture) Set aside.
When the squash is cool enough to handle, scoop out 4 cups of the cooked flesh and add to a blender. Pour the cream in with the squash and blend until you have a smooth consistency. Add the contents of the blender to a a large pot.
Heat the squash mixture over medium-heat and add in the shredded sharp cheddar and Monterey jack cheese. Stir until cheese has melted and is smooth. Add in the butter, ground nutmeg, ground sage, onion powder, garlic powder, ground cayenne pepper, and sea salt. Continue cooking for 2-3 minutes, until the mixture is cooked through. Add in cooked macaroni and stir until well coated.
In a greased 9x13 casserole dish, add the mac and cheese mixture. Sprinkle the cracker mixture over the top and bake for 25-30 minutes, until golden brown and bubbly.