Char the halved onion and ginger piece over an open flame or under a broiler until slightly blackened to release deep aromatics.
In a large pot, toast the star anise and cinnamon stick over medium heat for 2 minutes until fragrant.
Add the beef bone broth, charred onion, ginger, and fish sauce to the pot; 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.
Thinly slice the raw beef eye of round against the grain into paper-thin pieces (freezing for 15 minutes beforehand helps with slicing).
Remove the large aromatics from the broth and season with sea salt and black pepper.
Place the cooked noodles in a large bowl and layer the raw beef slices on top.
Pour the boiling hot broth over the beef to cook it instantly, then top with bean sprouts, Thai basil, jalapeño slices, and a squeeze of lime.