Char the halved onion and sliced ginger in a dry pan over medium-high heat until fragrant and slightly blackened.
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 heat and simmer for 20 minutes to allow the aromatics to infuse the broth.
While the broth simmers, cook the brown rice noodles according to package directions, then drain and set aside.
Strain the broth through a fine-mesh sieve into a clean pot, discarding the solids, and stir in the fish sauce, sea salt, and black pepper.
Divide the cooked noodles into a large serving bowl and arrange the raw, very thinly sliced eye of round beef on top of the noodles.
Pour the boiling hot broth directly over the beef and noodles; the intense heat will cook the thin beef slices instantly.
Garnish the soup with fresh bean sprouts, Thai basil, cilantro, jalapeño slices, and a generous squeeze of lime juice before serving.