In a Dutch oven or casserole set over moderate heat melt the butter. Add the shallots and cook, stirring, for 3 minutes. Add the garlic cloves, thyme, onions, chicken stock and salt and pepper, bring to a boil on top of the stove and cover with foil and lid. Transfer Dutch oven to a preheated 325 degree oven and cook for 4 hours. Discard thyme.
In a blender puree soup, in batches, adding butter, a little at a time, until incorporated. Return to pan and heat until hot. Correct seasoning. Ladle soup into soup bowls and drizzle with truffle oil.