In a large dutch oven, on medium-high heat, heat the oil and melt the butter. Add the onions, bay leaves and thyme and sauté until the onions are translucent and starting to caramelize. About 10-15 minutes.
Add the red wine and deglaze the pot. Sprinkle in the flour and stir continuously to cook out the flour.
Add the beef stock and bring the soup to a boil, lower the heat and simmer for 20 minutes or so until the soup is thickens slightly. Season with salt and pepper. Discard the thyme sprigs and bay leaves.
Turn the oven on broil. Ladle the French Onion Soup into oven safe bowls. Slice the baguette into 3/4 inch slices and grate the Gruyere cheese.
Top each bowl with a layer of the baguette, a generous handful of cheese and place the bowls under the broiler for about 5 minutes until the cheese starts to bubble and brown.