Slice the shallots in 1/4 inch slices, down to the root end. Toss the sliced shallots (onions) in a light coating of olive oil, a few grinds of black pepper and a good sprinkle of kosher salt. Put in a non-stick roasting pan or oven proof skillet and set in a 350 degree oven. Now all you have to do is leave the onions for about 45 minutes. Don’t touch, don’t move, don’t shake – just leave them. This is what gives them caramalization – which gives them the depth of flavor that is needed for a great onion soup. It’s also what makes it a soup to make for quiet days – there’s not much to do! After the first 45 minutes, check the shallots, tossing to assess the browning. If there is just slight browning, return to the oven, checking every 10 minutes, until there is a lot of deep brown color, but not dried out or burnt.
Bring the beef stock, water, brandy, thyme and bay leaf to a simmer. Add the braised shallots, and simmer for 45 minutes then taste for salt and pepper. If using fresh thyme, remove the stems. Preheat your broiler to high.
As the broiler is heating up, time to prepare the cheese and bread – the two other components to this triumverate of a soup. Use the best Emmenthaler you can afford – this is a cave-aged Swiss Emmenthaler from a wonderful local cheese purveyor, Joppa Fine Foods. Because their artisinal cheeses vary by season I have used many different Emmenthalers for this soup, but always it is flavorful! My favorite way to use the cheese is to shred some to put directly on the soup, as well as full slices to place directly on the croutons.
Put some nice thick slices of baguette under the broiler as it is heating up, just to toast lightly on both sides. Ladle soup into some bowls or crocks, add the toasted baguette slices and cover with the shredded/sliced Emmenthaler. Place under the broiler until bubbly and lightly browned – just a few minutes.