Note: Beef Bourguignon tastes even better the next day, making it ideal for a make-ahead main course.
Preheat oven to 250 degrees Fahrenheit.
Before you start, prepare your mise en place, so you have everything ready when you need it. It's the key to less stressful cooking, and one I am often guilty of skipping. Do as I say, not as I do! lol Dice your bacon, cube your beef, wash and chop your veggies (except the mushrooms), and have all of your ingredients ready. Read through the entire recipe so you know that the mushrooms, pearl onions, and beurre manie are added after it spends several hours in the oven.
Cook the bacon over medium heat until crispy, then remove to a plate, leaving the fat in the pan. Pat the beef cubes dry, then season well with salt and pepper. Brown them in the bacon fat on all sides in batches until well browned, but not cooked through. Do not crowd the pan; you want them to brown, not steam. Remove to the plate with the bacon, and continue until all cubes are browned.
Add your diced onion and carrots, along with some salt and pepper, to the remaining fat and cook until the onions are translucent. Add the tomato paste and minced garlic and stir, cooking a minute or two, being careful not to burn the garlic. Stir in the thyme and the bay leaves.
Turn off the heat (for safety). Add the half cup of cognac, stirring to deglaze the pan. Turn the heat back to medium and cook for several minutes, until the cognac reduces. Add the meats back into the pot, stirring to combine. Pour in the entire bottle of red wine and enough beef broth to cover the meat by about an inch. I used 32 ounces in mine. Bring to a boil, then cover the pot and move it to the preheated oven for two hours. If you are making this ahead of time, let it cool, then refrigerate overnight. Continue with the next step the following day.
After two hours, check the beef cubes for tenderness and return to the oven, checking every 45 minutes, until the cubes are tender and pull apart easily. Near the end of the oven time, brown the mushrooms, prepare the beurre manié, and take the pearl onions out of the freezer.
Remove the lid and return to medium heat on the stovetop. Add the browned mushrooms and pearl onions, then add the beurre manié. Bring to a boil, then reduce and simmer to thicken and reduce the sauce a bit. Start your noodles or mashed potatoes, if desired. Taste the sauce for seasoning and adjust accordingly. Serve hot with toasted baguettes or over noodles or mashed potatoes.
Let leftovers cool and store for 5 days in an airtight container in the refrigerator.