1. Heat oven to 400 degrees. Pierce potatoes with a fork and bake at 400 degrees for 50 minutes until tender. Allow to cool slightly. Scoop potato flesh into a bowl and mash.
2. Meanwhile, cook bacon in a large nonstick skillet until crisp, about 8 minutes. Remove bacon and crumble; set aside. Reserve 2 tbsp of bacon fat.
3. In a large pot, add butter and reserved bacon fat. Heat over medium heat. Add onion and cook 3 minutes; sprinkle flour over onion and cook 1 minute. Gradually whisk in milk; stir in salt, pepper, nutmeg and cayenne. Add reserved mashed potatoes and bring to a simmer. Reduce heat to medium-low and simmer 10 minutes, stirring occasionally. Stir in 2 cups of the cheese, half the reserved bacon and half the scallions.
4. Heat broiler. Divide soup equally among 6 flame-proof onion soup crocks. Sprinkle remaining cup of cheese over tops of crocks. Broil 4 inches from heat source for 3 minutes until cheese melts.
5. Garnish each with 1 tsp sour cream and remaining bacon and scallions.