Place macaroni pasta and hot water into a large microwave safe bowl. Cover with plastic wrap and heat on high for 3 minutes. Stir and cover again. Return to the microwave to heat for 3 minutes on 50% power. Add butter and stir until melted.
Whisk together flour and milk in a cup until smooth, add to the bowl of cooked macaroni. Fold in cheese until melted. Season with salt and pepper. Cover and return to the microwave.
Cook for another 3 minutes on high powder. Let stand for 1 minute before stirring until smooth.