Pat the chuck roast dry with paper towels to help it brown properly. In a small bowl, mix the onion soup mix, black pepper, and most of the salt. Rub this mixture all over the roast so every side is coated evenly.
Heat one tablespoon of oil in your Dutch oven over medium heat. Place the roast in the pot and sear each side until deeply browned. This step locks in juices and builds a rich, savory crust.
Remove the roast temporarily and add the remaining oil. Add sliced onions and sprinkle with the remaining salt. Cook them slowly, stirring occasionally, until softened and lightly caramelized.
Pour in the red wine and scrape the bottom of the pot to lift all those flavorful browned bits. Let the wine simmer for a few minutes to slightly reduce. This step intensifies the sauce.
Pour in the beef broth and add fresh thyme. Return the seared roast to the pot, nestling it into the onions and liquid. Bring everything to a gentle simmer.
Cover the pot and transfer it to a preheated oven at 325°F (163°C). Let it cook for about 3 hours until the beef is fork-tender and easily pulls apart.
Remove the roast and shred it using two forks. Simmer the cooking liquid on the stovetop until slightly thickened. Return the shredded beef to the pot, top with Gruyère cheese, and broil briefly until melted and bubbly.