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Special equipment: four 12-ounce soup crocks
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For the soup: Melt the butter in a large Dutch oven or pot over medium heat.
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Add half of the onions and season with 1/4 teaspoon salt and a few grinds of pepper.
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Top with the remaining onions and season with 1/4 teaspoon salt and a few more grinds of pepper.
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Add the bay leaves and thyme.
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Cook, stirring occasionally, until all of the liquid evaporates the onions are very soft and just begin to turn golden, 45 minutes to 1 hour.
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Add the white wine, bring to a simmer and cook, stirring, until almost completely evaporated, about 6 minutes.
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Pour in the beef broth and 1 cup water, bring to a high simmer and cook until the soup has reduced to 5 cups, 30 to 40 minutes.
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Season with salt and a few grinds of pepper.
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Remove the bay leaves and thyme.
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Either keep warm on a low burner or cool completely, refrigerate and reheat later.
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(The soup can be made and refrigerated up to 2 days in advance or frozen for up to 1 month).
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For the mac 'n' cheese: Bring a medium pot of water to a boil, add the macaroni and cook according to package instructions.
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Drain, reserving 1/2 cup of the cooking liquid.
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Melt the butter in a medium saucepan over medium heat.
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Whisk in the flour until smooth, about 2 minutes.
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Gradually whisk in the milk and reserved pasta water and stir until thick, about 4 minutes.
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Stir in 1 cup each of the cheeses, 1/2 teaspoon salt and a few grinds of pepper; stir until melted and smooth.
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Remove from the heat and stir in the cooked pasta until coated.
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Let cool slightly, stirring frequently.
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Preheat the oven to broil.
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Place the soup crocks on a rimmed baking sheet and divide the hot soup among the crocks, filling about three-quarters of the way.
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Top each with a quarter of the mac 'n' cheese (some will sink into the soup, which is fine).
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Evenly sprinkle with the remaining cheeses and the panko.
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Broil until the cheese is melted and golden brown in spots, 2 to 3 minutes (the soup will bubble and some may spill out).
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Serve hot.