Heat oven to 350.
cut squash lengthwise in half;discard seeds.Remove peel.Cut each half crosswise into thin slices.
Place in a large saucepan.Add enough water to cover squash.
Bring to a boil on high heat;simmer on medium low heat 8-10 minutes,or until squash is tender.
Meanwhile,cook bacon in skillet until crisp;remove from skillet,reserving 1 Tablespoon drippings in skillet. Drain bacon.add onions to reserved drippings;cook and stir 5 minutes.Stir in flour and pepper and cook 1 minute.Add broth;cook and stir 3 minutes or until sauce is thickened. Remove from heat. Stir in 1 Cup cheese.
Drain squash. Arrange half in a 8" or 9" square baking dish; Cover with half the sauce.repeat layers; top with bacon and remaining cheese. Bake 25 - 30 minutes or until heated through.