Preheat a grill or grill pan to medium-high heat.
Add the apples, onions, beer salt and pepper in a medium pot or Dutch oven. Simmer until the apples and onions soften, a few minutes. Add in the brats and simmer until cooked through, about 10 minutes, turning once. Remove the brats from the liquid and reserve the beer braising liquid.
Brown the brats on the grill, covering with a metal bowl if using a grill pan, until you get nice grill marks on all sides, 5 to 6 minutes.
Place the brats on the buns and drizzle with some of the Beer Cheese Sauce. Top with the sauerkraut, some mustard and the jalapenos.
Add the cheese and mustard to a medium saucepan over medium heat. Stir until melted and smooth. Add the beer braising liquid and stir to combine. Add more braising liquid if the sauce is too thick; the sauce should be velvety.