Place oven rack in upper-middle position and preheat to 300°F.
Pat beef dry with paper towels. Stir together salt and pepper and sprinkle over beef. Heat 1 tbsp oil in Dutch oven until smoking. Add half of beef and cook without moving, 4-6 minutes, until well browned. Turn beef over and cook second side until well browned, another 4-6 minutes. If fat begins to smoke, reduce heat. Transfer beef to medium bowl. Repeat with remaining oil and beef.
Reduce heat to medium, add onion, and cook, stirring often, until softened and barely browned, 12-15 minutes. (If onions darken too quickly, add 1-2 tbsp water to pan.).
Add tomato paste and stir constantly until it browns on sides and bottom of pan, about 2 minutes. Add garlic and cook until fragrant, 30-60 seconds. Turn heat up to medium-high, add Guinness, and simmer, scraping up fond from sides and bottom. Add beef broth, carrots, prunes, thyme, and bay leaf. Add beef and any juices in the bowl. Cover and bring to a simmer. Transfer to oven and cook 2 to 2½ hours, turning meat twice with tongs during cooking. When done, a fork will slip easily in and out of meat.
Place water in a small bowl and sprinkle with gelatin. Let stand 5 minutes. Using tongs, transfer meat and carrots to serving platter; tent with foil. Strain cooking liquid through a fine strainer into a fat separator. Press on solids to extract as much liquid as possible, then discard solids. Allow to settle, then strain off fat. Return liquid to Dutch oven and reduce to 1 cup over medium heat, 5-10 minutes. Remove from heat and stir in bloomed gelatin; season with salt and pepper to taste. Pour sauce over meat and serve.