Place the halved onion and ginger piece cut-side down in a dry skillet over medium-high heat until deeply charred and aromatic.
In a large stockpot, lightly toast the star anise and cinnamon stick for 1-2 minutes until their oils are released and fragrant.
Pour the beef bone broth into the stockpot, add the charred onion, ginger, and fish sauce, then bring to a boil before reducing to a simmer for 20 minutes.
While the broth develops flavor, cook the rice noodles in a separate pot of boiling water until tender, then drain and rinse with cold water to prevent sticking.
Slice the beef eye of round against the grain into paper-thin slices; for easier slicing, place the beef in the freezer for 15 minutes prior to cutting.
Divide the cooked noodles into serving bowls and arrange the raw beef slices on top, seasoning lightly with sea salt and black pepper.
Strain the hot broth to remove solids and immediately pour the boiling liquid over the beef to cook it instantly.
Garnish the bowls with fresh bean sprouts, Thai basil, cilantro, sliced jalapeno, and a generous squeeze of lime before serving.