In a large resealable plastic bag, combine the beef brisket with the red wine, red wine vinegar, juniper berries, white peppercorns, carrots, celery, garlic, and 1 of the onions. Close the bag, pressing out any air and refrigerate the brisket overnight or for up to 2 days.

Preheat the oven to 275 degrees. Strain the marinade, discarding the solids. Pat the brisket dry. In a large enameled cast-iron casserole, heat the oil. Season the brisket with salt and pepper and cook over moderate heat until browned all over, 8 to 10 minutes. Transfer the brisket to a large plate. Add the remaining 3 onions and the 2 finely chopped apples to the casserole and cook over moderate heat, stirring frequently, until softened, about 7 minutes.

Return the brisket to the casserole and add the raisins, bay leaf, thyme, and the strained marinade. Season with salt and pepper and bring to a simmer. Cover and braise in the oven for about 3 hours, until the meat is very tender; turn the brisket halfway through cooking.

Carefully transfer the brisket to a plate; cover and keep warm. Strain the cooking liquid into a heatproof measuring cup, pressing down on the solids. Wipe out the casserole and add the cooking liquid and chicken stock. Boil over moderately high heat until reduced by half, about 20 minutes. Season the sauce with salt and pepper. Thinly slice the brisket across the grain and garnish with the chopped apple. Serve with the sauce.

The brisket can be refrigerated in the sauce, whole or sliced, for up to 2 days. Rewarm in the oven.