Place the onion and ginger in a dry skillet over medium-high heat until they are deeply charred and fragrant.
In a pot, combine the beef bone broth, charred onion, charred ginger, star anise, and cinnamon stick.
Bring the broth to a boil, then reduce heat and simmer for 20 minutes to infuse the aromatics.
Cook the rice noodles in a separate pot of boiling water until tender, then drain and place in a large serving bowl.
Slice the raw flank steak against the grain into very thin strips; for easier slicing, freeze the meat for 15 minutes first.
Strain the aromatics from the broth, return the liquid to the heat, and stir in the fish sauce, sea salt, and black pepper.
Arrange the raw beef slices over the noodles in the bowl.
Pour the piping hot broth directly over the beef to cook it through until it is no longer pink.
Top with bean sprouts, cilantro, and basil, then serve with a fresh squeeze of lime.