Fry the bacon in 1 tbsp of melted butter over medium - high heat until super crispy. Set aside on some paper towels then give a rough chop when cool so there's a mixture of crumbs and bigger pieces
Over medium - high heat, melt the remaining 2 tbsp butter in a medium saucepan then add the flour and whisk into a paste for a minute to cook the flour off.
Turn the heat down and add the milk gradually whisking vigorously to incorporate, making sure you are getting the flour paste from the bottom and sides of the pan. Add ¼ cup more milk if you think it will be too thick.
Continue to cook, whisking until it begins to gently simmer then turn the heat down to low before adding the cheese in three lots, whisking in between each lot making sure it has melted in before adding the next.
Add the black pepper and most of the bacon pieces (reserve a sprinkling for the top)
Add in your cooked pasta and the fresh thyme and let it gently bubble away for a minute in the sauce. Add a splash of pasta water if you feel like you need to loosen the sauce.
Serve with a sprinkling of bacon and thyme on the top.