Rinse the leeks very well. Chop all of the white and light green parts into one inch pieces. Heat a large saute pan on medium heat and saute the bacon until it's golden brown. Remove the bacon pieces and put them in a gratin or baking dish.
Saute the leeks in the pan with the bacon fat. If your bacon is particularly lean, you can add a bit of butter. Sprinkle in some salt and pepper. Cook the leeks until they begin to soften and wilt (about 15 minutes). It helps to partially cover the pan with aluminum foil or a lid, stirring often so they don't burn. Once the leeks have softened, put them in the gratin pan with the bacon pieces.
Preheat the oven to 375
Heat the butter and flour in a saucepan until it starts to foam. Stir often. Add the milk. Continue stirring to prevent scorching. Add the half and half. Cook until it's creamy and thick, stirring the entire time. Remove from heat and add the nutmeg, 1/4 teaspoon of salt, pepper and fresh thyme.
Add the cream sauce to the baking pan with the leeks and the bacon and toss until everything is well coated. Sprinkle the cheddar cheese on the top. Bake in the middle part of the oven for 30 minutes or until everything is brown and bubbly. You may also wish to put the pan under the broiler for just a bit to brown the top. Sprinkle more fresh thyme on the top. Let it rest for 10 minutes before serving. Enjoy!