How to Make It
Gather the ingredients.
Place bacon in a large deep Dutch oven skillet and cook over medium-high heat, turning occasionally, until evenly browned, about 10 minutes. Remove bacon with a slotted spoon and set aside.
Add onions and a generous pinch of kosher salt to the rendered fat. Allow to cook over medium-low heat, stirring often, until onions are deeply caramelized, about 40 minutes. As onions cook, you may need to add water ¼ cup at a time, to keep the onions from burning. After 40 minutes, the onions should be deeply browned and jammy in consistency. Once the onions have reached the desired color and consistency, remove from heat and set aside.
Meanwhile, about 20 minutes after the start of cooking time for the onions, bring a large pot of generously salted water to a boil. Add pasta and cook for 5 minutes. Drain and return pasta to the pot.
Preheat the oven to 350 degrees F (175 degrees C). Grease a 9x13-inch baking dish with butter.
Melt 4 tablespoons butter in a deep skillet over low heat. Add flour and cook until flour turns golden brown and smells nutty, about 2 minutes. Slowly add milk, a little at a time, while whisking constantly. Once all the milk has been incorporated, increase heat to medium and cook, stirring constantly, until sauce has thickened and can coat the back of a spoon, 10 to 12 minutes.
Remove sauce from heat and stir in mustard, hot sauce, nutmeg, a pinch of salt, Cheddar cheese, and gruyere cheese. Whisk until cheese is fully melted.
Add cheese sauce, reserved bacon, caramelized onions, and scallions to pasta. Fold in with a rubber spatula until everything is well incorporated. Season with salt and pepper. Transfer pasta to the prepared baking dish.
Melt the remaining 2 tablespoons of butter in a small skillet over medium heat. Once melted, add Panko breadcrumbs and cook until toasted and golden brown, 3 to 4 minutes. Top mac and cheese with toasted breadcrumbs.
Bake in the preheated oven until cheese has melted and top is lightly browned, about 30 minutes.
Turn on the broiler and broil on high until the top is bubbly and brown, 1 to 2 minutes.
Remove from the oven and let cool slightly. Finish with a pinch of flaky salt and black pepper and serve warm.
