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Meanwhile, melt the butter over medium heat in a medium skillet. Add the onions and saute until tender, about 3 minutes. Add the mushrooms and continue to saute until the mushrooms are beginning to turn golden around the edges, about 7 minutes. Add the Marsala. Scrape the brown bits off the bottom of the pan and cook until the Marsala has reduced by half, about 5 minutes. Add the mushroom mixture to the orzo in the large bowl. Add the cream, fontina, mozzarella, peas, salt, and pepper. Stir to combine. Pour the mixture into the prepared baking dish.
In a small bowl combine the bread crumbs, Parmesan, and dried thyme. Sprinkle the bread crumb mixture on top of the pasta. Bake until golden, about 25 minutes.