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Preheat the oven to 350 degrees F (180 degrees C). Grease a 2-quart baking dish.
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Bring a large pot of water to a boil and cook noodles for 1 or 2 minutes less than the package recommends for al dente. Drain, rinse with cold water, drain again, and set aside.
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Heat olive oil and butter in a large nonstick skillet over medium heat. When butter stops sizzling, add shallots and cook, stirring, until softened, about 2 minutes. Add garlic, red pepper flakes, and thyme and cook just until garlic is fragrant, 30 seconds to 1 minute.
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Stir in flour and cook, stirring, until flour bubbles, about 2 minutes. Add chicken broth, milk, cream, chicken bouillon granules, and tomatoes. Season to taste with salt and pepper. Cook, stirring, until thickened, 4 to 5 minutes.
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Add cooked chicken, noodles, and 1/2 cup grated Parmesan cheese. Stir well, and pour into prepared pan.
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Combine remaining Parmesan cheese with panko breadcrumbs and sprinkle evenly over the casserole.
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Bake in the center of the preheated oven until bubbly and lightly browned, about 30 minutes. Allow casserole to cool for 5 to 10 minutes, garnish with fresh basil, and serve warm.