Preheat the oven to 350 degrees Fahrenheit.
Heat to a boil a pot full of water (lightly salted), then add the pasta. Cook the pasta to al dente. Drain the pasta and place to the side.
Add the flour to the jalapeño and continue to stir until the mix turns pasty and lightly browns (approximately 2 minutes).
Transfer half the pasta and sauce into a baking dish, then layer half of the remaining cheese slices over top. Pour in the rest of the pasta and sauce atop the cheese.
Bake the mac and cheese for 15 minutes, then (optional) place the remaining cheese slices atop of the dish, spread evenly. Bake for an additional 1 to 2 minutes to melt and lightly brown.
Remove the mac and cheese from the oven and allow it to cool for 5 minutes. Serve.