Char the yellow onion and fresh ginger over an open flame or under a broiler until blackened and aromatic.
In a large pot, toast the star anise and cinnamon stick over medium heat for 1-2 minutes until fragrant.
Add the beef bone broth, charred onion, charred ginger, and fish sauce to the pot and simmer for 20 minutes.
While the broth simmers, cook the rice noodles according to package directions, then drain and set aside.
Strain the broth through a fine-mesh sieve to remove all solids and return the clear liquid to the pot to boil.
Place the cooked noodles and the raw, very thinly sliced flank steak into a large serving bowl.
Pour the boiling broth directly over the beef and noodles to cook the meat instantly until it turns pale pink.
Top the soup with bean sprouts, Thai basil, jalapeño slices, lime juice, sea salt, and black pepper before serving.