Preheat the Oven – Set to 350°F (175°C). Lightly grease a 9x13-inch baking dish.
Cook the Aromatics – In a large skillet, melt butter over medium heat. Add onion and sauté until soft (about 3 minutes). Stir in garlic and cook for 30 seconds.
Make the Roux – Sprinkle flour over the onion mixture and stir for 1 minute to remove the raw flour taste.
Create the Sauce – Slowly whisk in milk until smooth. Stir in sour cream, 3 cups shredded cheese, red pepper flakes, salt, and pepper. Cook until the cheese melts and the sauce thickens.
Combine – In a large bowl, mix cooked pasta, chicken, and the cheese sauce until evenly coated.
Assemble – Spread mixture into the prepared baking dish. Sprinkle remaining cheese over the top.
Bake – Cook uncovered for 20–25 minutes, until bubbly and golden.
Serve – Let rest for 5 minutes before serving for easier scooping.