1. First, prep your onions: remove the ends and the outer layers; halve and thinly slice.
2. Bring a large soup pot to medium-high heat and drizzle in your olive oil. Add your sliced onions and place a lid on the pot; cook until the onions are translucent, about 20 minutes. When they are tender, remove the lid and continue to sauté the onions until they are golden brown and caramelized. (Be careful not to let them burn.)
3. Carefully pour in the whiskey (slowly, to lessen the risk of the alcohol flaming up), white wine, dried bay leaves, and fresh thyme. Cook until the liquid has reduced by half.
4. Now add the beef broth, reduce the heat to medium-low, and let simmer for 1-2 hours.
5. As the soup simmers, prep the croutons: Preheat the oven to 400 degrees. Cube the bread into large chunks, spread on a cookie sheet, drizzle with olive oil, and season with salt and pepper. Pop into the oven for 5-10 minutes, until the bread starts to crisp. Once the first side is toasted, remove from the oven and flip; return to the oven.
6. When the croutons are crispy on all sides, remove from the oven and generously shred the gruyere on top.
7. As the cheese melts onto the toast, season the soup with salt and pepper to taste. Ladle it up and mound the gruyere croutons over each serving. Serve right away.