Preheat the oven to 400 degrees F.

Cook pasta in a large pot of boiling salted water according to package directions for al dente.

Drain the pasta and place it back into the cooking pot.

Cook the bacon until crispy in a Dutch oven set over medium heat.

Remove the bacon to a paper towel lined plate to drain, leaving 2 tablespoons of the drippings in the pot. 

Add the butter to the bacon fat and allow it to melt, then add in the flour and whisk constantly for 1-2 minutes, until golden brown. 

Gradually whisk in the milk, salt, pepper, and nutmeg and continue cooking for about 5 minutes, whisking often until the mixture begins to thicken. Remove the pot from the heat.

Fold in ¾ cup each of the cheddar and Gruyere, a little at a time, until completely melted.

Add the cooked pasta and bacon and stir until well combined.

Top the pasta with the remaining cheese, transfer the pot to the oven, and bake for 15-20 minutes, uncovered, until the cheese is bubbly and melted on top.