Place the beef bones in a large stockpot and add enough water to cover. Place over high heat and bring to a boil. Once boiling, cook for 5 minutes, then drain.
Rinse the bones and the pot well under cold water. Place the bones back in the now empty pot.
Add the brisket, the 6 quarts (5.5 liters), and salt to the pot. Bring to a boil, then reduce heat to a simmer.
Cook, occasionally skimming any froth and impurities from the top, for 3 hours.
Remove the pieces of cooked brisket and place in a bowl. Cover and refrigerate until needed (to add a few pieces to the Phở).
Arrange the unpeeled onions and ginger on a baking sheet. Place under the broiler over high heat and cook, turning as needed, until charred on all sides. Remove from heat.
Once cool enough to handle, remove the peel from the onions and ginger. Brush off any charred spots and rinse under water. Add the vegetables to the simmering stockpot and simmer for another hour.
Place a skillet over medium heat. Add the cloves, star anise, cardamom, coriander, and cinnamon to the hot pan. Cook, stirring constantly, until fragrant, but not burned. Remove from heat.
Place the toasted spices in a spice bag, close, and add to the stockpot. Continue to cook, uncovered for one last hour.
Skim off any remaining froth or excess fat that develops on top and discard the bones, onion, ginger, and spices.
At the end of cooking, add the rock sugar, fish sauce, and adjust seasonings with salt as needed. Remove the pot from heat.
Strain the broth through a fine mesh strainer into a large container. If it is not completely clear, strain again.
If not using the broth immediately, allow to cool, cover, and refrigerate until ready to use.