Preheat oven 350 degrees.
Put a pot of water on for the pasta. Cook pasta according to package directions. While water is coming to a boil begin making the cheese sauce.
Melt butter in a large pot over medium heat, add in minced onion and cook until onion is almost done.
Stir in minced garlic and minced chipotle peppers in adobo sauce. Cook two minutes stirring constantly.
Whisk in six tablespoons of flour. Cook two minutes whisking constantly.
Whisk in milk a little at a time. When mixture starts to thicken, add in more milk, repeat until all the milk is added in.
Turn down the heat a little and whisk in cheddar and Monterey jack cheeses. Stir to combine as cheese melts.
Taste the cheese sauce for salt and black pepper.
Turn off heat, stir in cooked drained pasta, and a drained can of corn (optional).
Transfer spicy macaroni and cheese into a 9" x 13" pan sprayed with non-stick cooking spray.
Tightly cover macaroni and cheese with foil.
Bake at 350 degrees for 45 minutes.
Remove cover and bake an additional 15 minutes or until mac n cheese is browned to your liking.