In large pan/skillet melt butter and sauté onions and habaneros until translucent. Sprinkle in flour mixing everything together.
After about 1 minute slowly start whisking your heavy cream in. Constantly stir for about 5 minutes to allow to thicken.
Reduce heat and add in shredded cheese, seasoning and bacon. Cook until cheese is completely melted, then pour in cooked pasta and stir until shells are coated.
Pour into a 9x13 baking dish and bake for about 10 minutes.