1. In a large pot, melt the butter over medium-high heat. Add the onions and cook, stirring occasionally, until softened and lightly browned, about 10 minutes.
2. Add the flour and stir until combined. Gradually add the beef stock, stirring until combined.
3. Add the thyme, salt, and pepper. Bring to a boil, reduce heat to low, and simmer for 30 minutes.
4. Add the brandy and stir to combine. Simmer for another 10 minutes.
5. Ladle the soup into shallow soup bowls, top with the Gruyere cheese and parsley, and serve.