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Preheat oven to 375 degrees.
Butter an 8-inch-square (1 1/2 quart) baking dish or pan. Set aside.
Fill a 4- to 5-quart pot about three-quarters full with water and add 1 tablespoon salt. Bring to boil and add the pasta. After 8 minutes, add the broccoli. Cook, stirring once or twice, until both pasta and broccoli are tender but firm, 3 to 4 minutes more. Drain and reserve the pot.
In medium skillet, melt 2 tablespoons butter over medium heat. Cook onion, stirring occasionally, until soft, about 5 minutes. Add the mushrooms and cook until soft and creamy in texture, 6 to 8 minutes. Sprinkle with salt and black pepper to taste. Set aside.
Using same pot as pasta, melt remaining 2 tablespoons butter over medium heat. Slowly whisk in flour and whisk constantly until a paste forms, 30 to 45 seconds. Continue whisking for 1 to 2 minutes more, until mixture starts to darken slightly.
Slowly whisk in milk, cream and 1/2 teaspoon salt and cook until mixture starts to thicken and is just beginning to bubble around edges, 5 to 7 minutes. Add 2 1/2 cups Cheddar, the cayenne, mustard powder and nutmeg; stir until sauce is smooth but not runny.
Add pasta-broccoli mixture and stir to combine. Pour into prepared baking dish. Distribute crispy fried onions across pasta, and top with remaining Cheddar.
Place dish on rimmed baking sheet and bake until bubbling and golden brown, about 30 minutes. Let cool for 15 minutes before serving.