Char the halved onion and ginger over an open flame or under a broiler until blackened and fragrant.
In a large pot, toast the star anise and cinnamon stick over medium heat for 2 minutes until aromatic.
Add the beef bone broth, charred onion, charred ginger, and fish sauce to the pot; bring to a boil, then 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 beef eye of round against the grain into paper-thin pieces.
Strain the broth through a fine-mesh sieve to remove the solids and return the clear liquid to the pot, keeping it at a rolling boil.
Divide the cooked noodles between deep bowls and top with the raw beef slices.
Pour the boiling broth over the beef to cook it instantly, then garnish with bean sprouts, cilantro, Thai basil, jalapeno slices, a squeeze of lime, and black pepper.