1Preheat oven to 350 F.
In a heavy sauce pan, melt butter, add onions, salt and pepper. Cook until onions are transluecent. Add red pepper flakes and cook a minute more. Add flour and stir mixture for one minute.
2Pour some of the milk (1 Cup) into the flour mixture whisking constantly until it smooths out. pour in the remaining milk, stirring constantly until it begins to thicken.
3Add garlic powder and thyme. Continue stirring and add the tuna. Add 1 1/2 cup of cheese and stir until completely melted. Taste to see if more spices is needed.
4Pour mixture into a casserole dish and stir in the elbow macaroni until cheese mixture is thoroughly coats the macaroni.
5Top with the remaining cheese and cracker crumbs.
Mix the butter and garlic powder and pour it over the cracker crumbs.
Bake for 30 minutes or until bubbly.