Meanwhile, in a large skillet, heat oil over medium-high heat. Add Swiss chard and onion; cook and stir 4 minutes. Add garlic; cook 2 minutes longer. Stir in tomatoes, beans, salt, pepper flakes, fennel and pepper. Cook 3-4 minutes longer or until chard is tender.
Drain rigatoni, reserving 1/4 cup pasta water. Add rigatoni, pasta water and basil to skillet; toss to combine. Serve with cheese.