Preheat oven to 350 degrees F (175 degrees C).
Bring a large pot of lightly salted water to a boil. Add pasta and cook. With 6 to 8 minutes left on the pasta, stir in broccoli, mushrooms and green peppers, and cook 6 to 8 minutes more, or until pasta is al dente; drain.
Meanwhile, melt butter in a medium saucepan over medium-high heat. Saute onions and garlic for 1 to 2 minutes. Stir in flour and milk; cook 5 minutes, or until mixture coats the back of a spoon. Remove from heat and stir in 1/2 cup Parmesan cheese, salt and pepper, to taste.
Spray a 9 by 13 inch-baking dish with cooking spray. Combine pasta, vegetables, milk mixture and 4 tablespoons basil in the prepared pan. Top with 2 tablespoons Parmesan cheese, and remaining 1 tablespoon basil. Place the baking dish into the oven and bake for 20 minutes, or until the top gets crispy.