Pre-boil the beef bones: Place beef bones in a large pot with water and bring to a rolling boil. Boil vigorously for 10-15 minutes, then drain the water, rinse the bones thoroughly under cold water to remove impurities, and scrub them clean.
Char the aromatics: Cut 2 large onions in half and the ginger into thick slices. Place them on a baking sheet and broil or grill until slightly charred and fragrant. Alternatively, you can char them directly over an open flame.
Toast the spices: In a dry pan over medium heat, toast star anise, cinnamon sticks, black cardamom, cloves, coriander seeds, and fennel seeds until fragrant, about 2-3 minutes. Be careful not to burn them. Place the toasted spices in a spice bag or cheesecloth.
Start the broth: In the large pot with the cleaned beef bones, add beef chuck or oxtail, charred onions, charred ginger, the spice bag, water, fish sauce, salt, and rock sugar. Bring to a boil, then immediately reduce heat to a very low simmer. Skim any foam that rises to the surface.
Simmer the broth: Continue to simmer the broth for at least 4 hours, or preferably 6-8 hours, maintaining a gentle simmer. This long simmering time extracts maximum flavor from the bones and spices.
Remove and slice cooked beef: After about 2-3 hours of simmering, carefully remove the beef chuck or oxtail from the broth. Let it cool slightly, then slice it against the grain into thin pieces. Return the sliced beef to the broth or set aside for serving.
Strain the broth: Once the broth has simmered sufficiently, remove the bones, charred aromatics, and spice bag. Strain the broth through a fine-mesh sieve or cheesecloth to ensure it's clear. Taste and adjust seasoning with fish sauce, salt, or rock sugar as needed.
Prepare the garnishes: Slice the remaining large onion very thinly. Chop green onions and cilantro. Slice limes into wedges and jalapeño/chili into thin rounds. Wash Thai basil, mint, and bean sprouts.
Cook the noodles: Bring a pot of water to a boil. Blanch the flat rice noodles according to package instructions, usually for 30-60 seconds, until tender but still firm. Drain thoroughly.
Assemble Phở: Divide the cooked rice noodles among serving bowls. Arrange the thinly sliced raw beef and cooked beef (if using) on top of the noodles. Ladle the piping hot broth over the beef and noodles; the heat of the broth will cook the raw beef.
Garnish and serve: Serve immediately with a side plate of fresh garnishes: sliced onions, green onions, cilantro, Thai basil, mint, lime wedges, bean sprouts, and jalapeño/chili slices. Offer hoisin sauce and sriracha sauce on the side for diners to add to their taste.
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