Combine the butternut squash, onion, coconut oil and garlic in a 9 x13 inch baking dish. Bake 40 minutes or until the squash is tender. Halfway through cook time, stir mixture.
While the vegetables bake, cook the pasta according to the box directions. Drain and return to the pot. Stir in the cream cheese until it’s completely melted. Add the cheese packets to the pasta and milk. Stir until well blended. Lastly, stir in the ham.
Add the pasta mixture to the vegetables, stirring to combine.
Top with the shredded cheese and crushed Cheddar Bunnies, then bake for 20 minutes, or until heated through.