Place the onion and ginger directly over a gas flame or under the broiler until charred and aromatic.
In a large pot, lightly toast the star anise and cinnamon stick over medium heat for 2 minutes until fragrant.
Add the beef bone broth, charred onion, and ginger to the pot; simmer gently for 20 minutes to infuse the flavors.
While the broth simmers, prepare the rice noodles according to package directions, then drain and set aside.
Slice the beef eye of round against the grain into paper-thin slices; for easier slicing, freeze the beef for 15 minutes first.
Remove the solids from the broth using a slotted spoon and stir in the fish sauce, sea salt, and black pepper.
Divide the cooked noodles and raw beef slices into a large bowl, then pour the boiling hot broth over the beef to cook it instantly.
Garnish the soup with bean sprouts, cilantro, Thai basil, jalapeño slices, and a squeeze of fresh lime juice.