Peel and dice the butternut squash. Reserve the seeds from the pulp if using. Rinse the seeds and transfer to a towel to dry. Set aside. Peel and dice the shallots, mince the garlic, and slice the leeks. For the fennel, trim the stalks from the bulb. Remove the core and dice the fennel bulb. Reserve some of the fronds for garnish. Peel, core, and dice the apples. Tie the fresh thyme, sage, and bay leaves together to make a bouquet garni and set aside.
In a large, heavy bottomed pot, heat the olive oil over medium heat. Add the shallots and leeks and sauté for 3 to 4 minutes until they soften and begin to brown. Add the minced garlic and sauté for 30 seconds. Add the kosher salt, nutmeg, and pepper and briefly sauté.
Add the diced squash, fennel bulb, and apples to the pot along with the broth and Pernod. Add the bouquet garni to the soup and bring to a simmer. Cook the soup on a low simmer for 15 to 20 minutes until the vegetables are very tender.
Meanwhile, preheat the oven to 325°F. Transfer the washed squash seeds to a small baking sheet. Combine the kosher salt, onion powder, cayenne, and pepper in a small bowl. Drizzle the seeds with the olive oil and sprinkle with the seasoning. Toss the seeds to coat.
Roast the seeds for 10 minutes. Stir the seeds on the pan and then continue roasting for another 5 to 10 minutes until they are browned and toasted. Set aside to cool.
When the vegetables are tender, purée the soup. Remove and discard the bouquet garni. Carefully transfer about half the soup to a blender. Cover and blend until smooth. Pour into a separate container. Repeat with the remaining soup. Rinse the soup pot and return the puréed soup to the pot. Reheat the soup and taste for seasoning, adding a bit more kosher salt if needed.
To serve the soup, pluck some of the reserved fennel fronds. Ladle the soup into bowls. Top with a drizzle of cream. Sprinkle with the roasted squash seeds and a dusting of fennel pollen. Top with a few fennel fronds and enjoy!
Notes
*Substitute with ⅓ cup pepitas if you don't have squash seeds