Place the apples, onion, beer, salt and pepper in a large pot over medium-high heat.
Simmer until the apples and onions are soft.
Add the bratwurst and let simmer 5 minutes per side.
Remove the brats to a plate. Reserve the braising liquid for the beer cheese sauce.
Grill bratwurst 5-6 minutes per side.
Serve bratwursts on buns, topped with the cheese sauce, kraut, Dijon mustard and jalapenos.