Place the whole spaghetti squash on a lined baking sheet and bake at 350° for 90 minutes. Cut the squash in half lengthwise and reserve half for another use. Using a fork, scrape the squash from the skin and set aside.

While the squash is baking, in a medium saucepan melt butter over medium heat. Add the flour and whisk until well combined. Cook for 1-2 minutes and very slowly incorporate the milk, whisking vigorously after each addition. After all the milk is well incorporated add the chipotle pepper and cook for an additional 5 minutes or until it has thickened.

Add the goat cheese and using an immersion blender, blend the mixture until smooth. Add the squash and fold into the sauce so it is all coated. Top with shredded cheese and parsley. Cover and cook for a couple minutes allowing the cheese to melt. Serve immediately.