With a sharp knife or fork, prick each sausage several times. In a large pot, combine the red onions and beer and bring to a simmer over medium heat. Add the bratwursts and poach until almost cooked through, about 5 minutes. Remove the sausages from the liquid and set aside, reserving the liquid.
In a large pot, cook the bacon over medium heat until crisp, about 5 minutes. If there's a lot of grease, pour some off.
Add the yellow onions to the fat in the pan and cook, stirring, until soft, 5-6 minutes. Add the garlic and cook for another 30 seconds. Add the apples, the bay leaf, peppercorns, and juniper berries.
Finally add the drained sauerkraut and 3-4 soup ladles of the reserved beer that the brats cooked in. Reduce the heat and simmer for about an hour, stirring occasionally and adding more reserved beer if needed.
Preheat the grill. Grill the sausages until cooked through and brown on the outside. Place the grilled sausages on top of the sauerkraut in the pot and serve.
Serve with mashed potatoes, if desired, plenty of bread or pretzels, and of course, a selection of mustards!