Char the halved onion and sliced ginger over an open flame or under a broiler for 5 minutes until slightly 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, and ginger to the pot; bring to a boil, then reduce heat and simmer for 20 minutes to develop the flavor.
While the broth simmers, cook the brown rice noodles according to package directions, then drain and set aside.
Thinly slice the raw flank steak against the grain into very thin pieces; for easier slicing, place the beef in the freezer for 15 minutes beforehand.
Strain the broth through a fine-mesh sieve to remove the solids and return the clear liquid to the pot, seasoning with fish sauce, sea salt, and black pepper.
Divide the cooked noodles into a large serving bowl and arrange the raw beef slices on top in a single layer.
Pour the boiling hot broth directly over the beef to cook it instantly, then garnish with bean sprouts, Thai basil, jalapeño slices, and a squeeze of fresh lime.