Place the sliced onions in the slow cooker and scatter the butter pieces over them.
Pour in the beef broth, then add the thyme, bay leaves, salt, and pepper.
Cover and cook on low for 8 hours, stirring once halfway through if possible.
When the soup is nearly done, arrange the baguette slices on a baking sheet and top each with shredded Gruyere.
Broil the topped slices for 1 to 2 minutes until the cheese melts and bubbles.
Remove the bay leaves from the soup, then ladle it into bowls and float two croutons on top of each serving.