Char the yellow onion and fresh ginger over an open flame or under a high broiler until the skins are blackened and fragrant.
In a large stockpot, toast the star anise and cinnamon stick over medium heat for 2 minutes until their aroma is released.
Add the beef bone broth, charred onion, ginger, and fish sauce to the pot and bring to a gentle simmer for 20 minutes.
While the broth simmers, cook the brown rice noodles according to package instructions, drain, and set aside.
Thinly slice the raw flank steak against the grain into paper-thin pieces to ensure they cook quickly in the broth.
Strain the broth through a fine-mesh sieve to remove the solids and return the liquid to the pot, seasoning with sea salt and black pepper.
Place the cooked noodles in a large bowl, layer the raw beef slices on top, and pour the boiling hot broth over the meat to cook it instantly.
Top the soup with mung bean sprouts, Thai basil, jalapeño slices, and a fresh squeeze of lime before serving.