Heat butter in a saucepan. Sauté the onions in the butter until translucent. Pour in water until onions are covered.
Cook over medium heat for about 2 hours, until onions caramelize. Add water if necessary.
Add apple and thyme and cook for 1 minute. Add flour, stirring, and sweat for 1 minute. Deglaze with white wine.
Pour in stock, add bay leaves and apple cider and simmer for 30 minutes. Season with salt and pepper and add a splash of brandy.
Serve with toasted bread and grated cheese.
Preparation Tip:
Instead of toasted bread, you can also serve the soup with, for example, herb bagels.