In a large, heavy stockpot, heat the 2 tablespoons of olive oil until shimmering. Add the onion, season with salt and pepper and cook over moderately high heat, stirring, until softened but not browned, about 6 minutes. Add 3 of the thyme sprigs and the bay leaf. Stir in the squash and the stock and bring to a boil over high heat, stirring frequently. Reduce the heat and simmer the soup for 15 minutes, stirring occasionally.