Cook the Squash
Place the halved and seeded spaghetti squash in a microwave-safe dish with a lid. Add about 1/4 inch of water to the dish. Cover and microwave on high for 10 to 12 minutes. Once it is cool enough to handle, use a fork to scrape the flesh horizontally to create long strands. Transfer the strands to a bowl.

Sauté the Aromatics
While the squash is cooking, melt the light margarine in a medium skillet over medium heat. Add the thinly sliced onion, red pepper flakes, garlic powder, salt, and black pepper. Sauté until the onions are thoroughly browned and caramelized, about 5 to 10 minutes.

Prep the Oven
Preheat your oven to 375°F (190°C). Grease a baking dish with nonstick cooking spray.

Combine the Mixture
In a bowl, mix the cooked spaghetti squash strands, the browned onion mixture, the fat-free sour cream, and 1/2 cup of the shredded light Cheddar cheese. Stir until well combined.

Assemble the Gratin
Transfer the squash mixture to the prepared baking dish and smooth the top. Sprinkle the remaining 1/2 cup of Cheddar cheese evenly over the casserole.

Bake and Broil
Bake in the preheated oven for 20 to 25 minutes until heated through. For a crispy crust, switch the oven to broil for the last 2 to 3 minutes, watching carefully until the cheese is golden brown.