In a large pot, over medium-high heat (if you want specifics I cooked on a 6-7) add the butter and onions, stir. Brown the onions for 30-40 minutes, stirring often. If you find that the onions are sticking too much to the bottom, add more butter or a splash or two of the beef broth.
Add the garlic and flour and stir for roughly a minute.
Now the fun part, add the whiskey and scrape the bottom of the pan. Get all the bits and simmer the alcohol down for 8-10 minutes, over medium height.
Next add the beef broth, bay leaves, thyme, Worcestershire sauce, sea salt, and pepper. Taste and if it's not rich add a heaping spoonful of beef bouillon (I used Better Than Boullion - get it at Costco or Amazon).
Simmer over medium heat for 35 minutes.
Preheat oven to 425F
Ladle the soup into french onion bowls, and top with the slices of the baguette. Layer on the cheese and bake for 5-10 minutes. Keep an eye on it so it doesn't burn, just until the cheese gets golden and bubbly.