First, bring a large pot of salted water to a boil and cook your pasta for about 2 minutes less than the package suggests. You want it slightly undercooked so it can absorb the cheesy goodness later. Drain it and set it aside.
Chop the bacon into small bits and toss it into a skillet over medium heat. Let it sizzle until crispy, then transfer to a paper towel-lined plate. Leave a bit of the bacon grease in the pan—it gives the sauce amazing flavor.
Add the butter to the same skillet. Once melted, stir in the chopped jalapenos and cook for a minute or two. They’ll soften up and mellow out, which helps them blend better into the sauce without overpowering it.
Now sprinkle in the flour and whisk it together with the butter and jalapenos. Keep stirring for about 1 minute to cook off the floury taste. Gradually pour in the half-and-half while whisking. Once it thickens slightly, add all three cheeses and stir until everything melts into a creamy sauce.
Add the cooked pasta and bacon into the skillet and stir gently to coat every piece with that cheesy sauce. Taste it, then add salt and black pepper as needed. You can leave everything in the skillet if it’s oven-safe or transfer it to a baking dish.
In a small bowl, mix together the melted butter, Panko breadcrumbs, and Parmesan. Sprinkle this mix evenly over the top of the pasta—it’ll bake into a perfectly crunchy crust.
Place your dish in a preheated oven at 350°F and bake for about 20 minutes. The top should turn golden, and the cheese sauce will bubble around the edges. Let it rest for 10 minutes before digging in so everything can set a bit.