Cut butternut squash in half, remove seeds, and brush 1 tablespoon of olive oil over the exposed flesh of each half.
On a half sheet pan or cookie sheet, bake for 1 hour 10 minutes or until a knife pierces the thickest part with very little resistance. Let cool for 20 minutes, remove flesh from the skin and cut into large cubes.
Meanwhile, heat 1 tablespoon of oil over medium heat until shimmering in a small skillet but not smoking. Add onion and garlic and saute, occasionally stirring, until onion turns transparent and garlic is fragrant about 5 minutes.
Add squash, onion and garlic mixture to a blender with rosemary, salt, pepper, stock and nutmeg. Pulse at first to bring the mixture together, then blend on high until smooth, about 1 minute. Warm in a large saucepan over medium heat until hot. Serve hot with a garnish of pumpkin seeds.