Preheat the oven to 375 degrees F. Bring a pot of salted water to a boil; add the pasta and cook until al dente. Drain the pasta.
Melt the butter in a large saucepan over medium heat. Whisk in the flour and cook, whisking constantly for about 2 minutes, then slowly whisk in the milk. Add the salt and nutmeg and simmer, whisking occasionally, until thick, about 8-10 minutes.
Stir in 1 1/2 cups cheddar, ¾ cup Gruyere and ¾ cup Fontina until melted. Add the pasta, half of tomatoes and half of fresh mozzarella and stir until incorporated with cheese sauce.
Add the pasta mixture to a buttered 2-quart baking dish and top with the remaining gruyere, fontina, tomatoes and fresh mozzarella. Sprinkle with the toasted panko breadcrumbs and bake for about 20 minutes.
After baking, top with ¼ cup chopped basil.