• Preheat the oven to 300°F.

Sear the brisket

• Season the brisket on both sides with salt, onion powder, and a few grinds of black pepper.
• Coat the bottom of a heavy braising pan with 1 tablespoon of olive oil and set over medium-high heat. Sear the brisket until browned, about 4 minutes per side. Transfer to a plate and set aside.

Prepare the braising liquid

• Add the remaining 2 tablespoons of olive oil to the pan and reduce the heat to medium. Add the minced shallots and garlic and cook until softened and aromatic, about 2 minutes.
• Scatter 2 tablespoons of the flour evenly over the shallots and garlic. Using a spatula, scrape up any browned bits that may have accumulated on the bottom of the pan. Continue cooking until the flour is well incorporated and beginning to turn golden.
• Whisk in the water, then bring the mixture to a gentle simmer and cook until slightly thickened, about 3 minutes. Slowly whisk in the wine and orange juice and continue whisking until smooth.
• Zest the whole orange and add it to the sauce along with the fresh rosemary, thyme, and bay leaves. Bring the mixture to a gentle simmer and cook, stirring often, for 3 minutes. Return the brisket to the pan.
• Cut 4 or 5 slices from the center of the orange you used for zest, lay them on top of the brisket, and top with fresh thyme sprigs. Squeeze the juice from any remaining orange pieces over the top, then spoon some of the sauce over the meat.

Braise the brisket

• Cover the pan and place it in the oven for 2-1/2 hours. Remove about every 45 minutes to baste the meat, spooning the braising liquid over the exposed surface. Re-cover and return to the oven.
• After the brisket has been cooking for about 2-1/2 hours, remove the pan from the oven and add the pearl onions. Re-cover and continue braising for 1 hour longer.
• Remove the meat from the braising liquid, place it on a carving board, and tent it with foil to keep it warm. Transfer the onions to a serving dish and set aside.

Make the sauce

• Pour the braising liquid into a gravy separator (or skim the fat from the top with a spoon). Transfer about a cup to a glass measure, then add the balance to a small saucepan.
• Make a slurry for thickening the sauce by whisking one tablespoon of flour into the reserved cup of braising liquid until blended.
• Set the saucepan over medium-high heat and slowly pour the slurry into the sauce while whisking continually until smooth and beginning to thicken. If necessary, repeat the process using a little more flour. Once the sauce consistency is to your liking, transfer it to a bowl or gravy boat.

Carve and Serves

• Carve the brisket against the grain into 1/4-inch thick slices. Transfer to a serving platter and spoon some of the sauce over the top. Garnish with pearl onions, some orange slices, and fresh herbs.