Char the halved yellow onion and fresh ginger over an open flame or under a broiler until the surfaces are blackened and fragrant.
In a medium pot, toast the star anise and cinnamon stick over medium heat for 1 minute to release their essential oils.
Pour the beef bone broth into the pot and add the charred onion and ginger. Bring to a boil, then reduce heat and simmer for 15 minutes.
While the broth simmers, place the dry rice noodles in a bowl of hot water for 8-10 minutes until tender, then drain and set aside.
Thinly slice the beef eye of round against the grain into paper-thin pieces; freezing the meat for 20 minutes beforehand makes this easier.
Strain the broth through a fine-mesh sieve to remove the solids, then return the clear liquid to the pot and stir in the fish sauce, sea salt, and black pepper.
Divide the cooked noodles between serving bowls and layer the raw beef slices on top of the noodles.
Ladle the boiling hot broth directly over the beef to cook it instantly, then garnish with bean sprouts, Thai basil, sliced scallions, and a squeeze of lime.