Gently sauté the onion and shallots in 1 tablespoon of olive oil without browning them. Add the fennel and apple. Season with pepper.
Stir in the fennel seeds and cover with stock. Simmer for 30 minutes. Add thyme and season with up to 1/2 teaspoon salt and more pepper to taste.
Transfer to a blender and purée, adding the remaining 2 tablespoons olive oil. Serve immediately with fennel fronds and diced apple garnish.