Place the halved onion and sliced ginger under a broiler or over an open flame until charred and fragrant.
In a small dry skillet, toast the star anise and cinnamon stick over medium heat for 2 minutes until the oils are released.
In a medium pot, combine the beef bone broth, charred onion, charred ginger, toasted spices, and sea salt. Bring to a boil, then reduce heat and simmer for 20 minutes.
While the broth simmers, prepare the rice noodles according to package instructions. Drain and set aside.
Place the beef eye of round in the freezer for 15 minutes to firm up, then slice it against the grain into paper-thin pieces.
Strain the broth through a fine-mesh sieve to remove the solids and return the clear liquid to the pot. Stir in the fish sauce.
Place the cooked noodles in a large bowl and arrange the raw beef slices on top in a single layer.
Pour the boiling hot broth directly over the beef slices to cook them instantly until they turn opaque.
Top the soup with bean sprouts, Thai basil, cilantro, and sliced chili. Serve immediately with a squeeze of fresh lime.