Heat oven and prep: Heat oven to 400°F. Cut the pumpkin in half, take out the seeds and stringy stuff. Brush cut sides with 2 tablespoons olive oil, add salt and pepper.
Cook the pumpkin: Put the cut side down on a baking sheet. Cook 45-50 minutes until you can poke it easily with a fork and the edges look a little brown. Let it cool before touching.
Cook onions: Heat the last 1 tablespoon oil in a big pot on medium heat. Add cut onion, cook 5 minutes until soft and see-through. Add garlic, cook 30 seconds more.
Mix everything: Scoop pumpkin meat from skins, add to pot with onions. Pour in vegetable broth, ginger, nutmeg, salt, and pepper. Let it bubble up hot.
Let it cook slowly: Turn the heat to medium-low, let it cook slowly for 15 minutes so all flavors mix together really good. Stir it sometimes so nothing sticks.
Make it smooth: Use a stick blender to mix the soup until it's totally smooth and creamy. Move it around in circles for 2-3 minutes until no lumps are left.
Add cream: Stir in heavy cream and fresh thyme if you have it. Let it cook 2-3 minutes more to get hot. Taste it and add more salt if needed before serving.