Place the halved onion and sliced ginger in a dry skillet over medium-high heat until charred and fragrant.
Combine the charred aromatics, beef bone broth, star anise, cinnamon stick, tamari, sea salt, and black pepper in a large stockpot.
Bring the mixture to a boil, then reduce the heat to low and simmer for 20 minutes to develop the deep, savory flavors.
Cook the brown rice noodles in a separate pot of boiling water according to the package instructions, then drain and set aside.
Strain the broth through a fine-mesh sieve to remove the solids and return the clear broth to the pot to keep it at a rolling boil.
Divide the cooked noodles into large serving bowls and layer the raw, thinly sliced beef eye of round directly on top of the noodles.
Pour the boiling hot broth over the beef, which will cook the thin slices instantly to a tender medium-rare.
Serve immediately topped with fresh bean sprouts, cilantro, Thai basil, and a squeeze of lime juice.