Char the onion halves and ginger over an open flame or under a broiler until the skins are blackened and fragrant.
In a large pot, toast the star anise and cinnamon stick over medium heat for 2 minutes until the 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 rice noodles according to package instructions, then drain and set aside.
Thinly slice the raw flank steak against the grain into very thin strips to ensure tenderness.
Strain the broth through a fine-mesh sieve to remove the solids and return the clear liquid to the pot, seasoning with sea salt and pepper.
Divide the cooked noodles into a large bowl, top with the raw beef slices, and pour the boiling hot broth over the beef to cook it instantly.
Garnish the soup with bean sprouts, Thai basil, jalapeño slices, and a generous squeeze of fresh lime juice before serving.