Char the yellow onion and fresh ginger over an open flame or under a broiler until blackened and fragrant.
In a large pot, combine the beef bone broth, charred onion, ginger, star anise, and cinnamon stick.
Bring the mixture to a boil, then reduce the heat and simmer for 20 minutes to infuse the aromatic flavors.
While the broth is simmering, prepare the rice noodles according to the package directions and set them aside.
Place the raw, thinly sliced beef eye of round into a large serving bowl directly over the cooked noodles.
Season the broth with fish sauce, sea salt, and black pepper, then carefully remove the whole spices and aromatics.
Pour the boiling hot broth directly over the beef to cook it instantly until it is just tender and pink.
Top the soup with bean sprouts, cilantro, Thai basil, and scallions, then serve with a fresh lime wedge.