Slice onions, mince garlic, pull thyme off the stems.
In a large pot or dutch oven (my preference) heat to medium and add 3 tablespoons of butter.
Once the butter has melted and bubbled, add the onions, stirring to coat.
After a couple minutes, add the garlic. Now, be patient. Keep an eye on the onions and occasionally stir. The onions will shrink down and start to caramelize. This is a slow and happy process. If you stir too often, the onions will not release its sugar or brown. (see pics below).
After 20 minutes, the onions should be golden brown and soft. Increase to heat to medium-high and add the cognac and thyme. Stir well to deglaze the pot.
Next, add the beef broth. I prefer Better Than Bouillon for its depth of flavor in this soup.
Bring the soup up to a simmer and cook for 15-20 minutes.
While the soup is simmering, make your croutons. I like bite size croutons vs one large piece of bread because I think it’s easier to eat that way. Dice your bread and heat a large skillet on medium. Melt 1 tablespoon of butter and add bread cubes. Lightly salt and stir continuously until all the croutons are evenly toasted and golden brown. Remove from heat and set aside.
After the soup has simmered and reduced a little, give it a taste to check the salt. It may not need any because the beef broth has quite a bit, but check to be sure and adjust salt or pepper if necessary.
This last step can be done two different ways. Option 1) ladle soup into oven safe bowls. Top each serving with croutons and a large handful of shredded gruyere. Move your top oven rack to a height where your bowls will fit under broiler on a sheet pan. Set broiler to low. Place your assembled soup bowls on a sheet pan and put under the broiler. Keep an eye on it and watch as the cheese melts, bubbles, and browns. Remove from oven and let stand for a few minutes. They will be screaming hot. Option 2) assemble soup servings as mentioned above. Use a kitchen blow torch to melt and brown the cheese until golden brown and bubbling. (Also, blow torches are cool)