Pour 2 bottles of the beer into a medium (oven-proof) Dutch oven and bring to a boil.
Using a small knife or fork, pierce each sausage link several times.
Add bratwurst links to the beer, turn down the heat and simmer for 10 minutes.
Remove the sausages from the pan and set aside to cool slightly. Reserve the sausage-cooking liquid.
Slice the sausage links into 1-inch pieces and set aside.
Add the bacon to a separate dutch oven and cook over medium heat until crispy, about 8 to 10 minutes.
Remove the bacon with a slotted spoon and drain on paper towels.
Add the sliced bratwurst to the bacon drippings and cook until lightly browned, about 2 minutes.
Add the onions to the pan and cook, stirring often, until lightly brown and wilted, about 5 minutes.
Add the garlic and cook an additional 30 seconds.
Stir in the reserved sausage-cooking liquid, the remaining bottle of beer, chicken stock, potatoes, carrots, thyme, salt, pepper, and bay leaf to the pot. Bring mixture to a boil, reduce heat to a medium-low and cover.
Place the Dutch oven in the oven and bake for 30 minutes, or until the vegetables are tender.
Remove the bay leaf and thyme sprig. Stir the crispy bacon into the stew and serve hot with crusty bread.