Bring a large pot of lightly salted water to a boil. Add pasta and cook for 8 to 10 minutes. Stir in broccoli, mushrooms and green pepper, 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.
In a 9×13 inch baking dish combine pasta, vegetables, milk mixture and 4 tablespoons basil. Sprinkle with bread crumbs, 2 tablespoons Parmesan cheese, and remaining 1 tablespoon basil. Coat with butter flavored cooking spray.
Bake in preheated oven for 30 minutes, or until golden brown.