Bring a large pot of salted water to a boil. Cook the pasta according to instructions. Reserve 1/2 cup pasta water for the sauce.
While the pasta water is boiling, in a large skillet over medium heat, cook the bacon. Drain the bacon and reserve the fat for the sauce. If you want a lighter sauce, discard the bacon fat and add 1 Tbsp. olive oil instead.
When the bacon is done, remove from the pan and add the sage leaves. Get them crispy on both sides. Don't walk away, as this happens pretty quickly. Set aside the sage leaves.
While the pasta and bacon are cooking, chop the red onion, and shred the cheese. Measure the pumpkin and cream cheese.
To make the sauce, keep the pan on medium heat. Add the red onion, red pepper flakes, and smoked paprika, and cook for about 30 seconds, or until fragrant (making sure not to burn the red onion!). Add the pumpkin puree, cream cheese, nutmeg, and reserved pasta water. Stir and simmer for about 5 minutes to slightly thicken. Lower the heat if it is boiling heavily.
Cook the pasta until just under al dente, as we will finish cooking the pasta in the sauce. Drain your pasta and have it ready to go. Add the pasta and stir and cook for 2-3 minutes.
Serve immediately and top with crumbled bacon, shredded cheese, and crumbled crispy sage.