Pre-heat oven to 375°. Melt butter in a large skillet or dutch oven over medium-high; add onion and saute 2 minutes. Add the sausage and brown, using a wooden spoon to chop up and brown, about 10-12 minutes. Next, add apple and sage then cook about 5 more minute; add flour and then cook 2 more minutes. Add the cider and cook another 2 minutes, then add milk. Cook and stir occasionally, until thickened for about 8-10 minutes. Fold in half of the cheese, salt, and pepper making sure cheese completely melted.
Prepare pasta as directed, using large pot of boiling water. Drain pasta, then return to large pot and stir in cheese mixture. Spread the pasta in a greased 9 x 13" casserole dish and top with remaining cheese.
Bake for about 45 minutes. Let cool for 10 minutes before serving.