In stock pot, saute onions over medium heat. As onions begin to caramelize, scrape the browned debris from the pot. Continue until you are no longer able to remove the debris from the bottom. Do not rush this process; this makes the soup sweet and dark.
Once onions are dark brown and pan is covered with debris, deglaze with brandy; add chicken stock and thyme. Bring to a simmer; reduce uncovered 20 minutes. Season with salt and pepper. Spoon into individual serving dishes.
Top each dish with a crouton and one slice of cheese. Broil until browned. Serve immediately.