Char the onion and ginger over an open flame or under a broiler until slightly blackened to release their 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, charred ginger, and fish sauce to the pot. Bring to a boil, then reduce heat and simmer for 20 minutes.
While the broth simmers, cook the brown rice noodles according to package instructions, 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 prior to cutting.
Strain the broth to remove the solids and season with sea salt and black pepper.
Divide the cooked noodles into a large bowl and lay the raw beef slices on top in a single layer.
Pour the boiling hot broth directly over the beef slices to cook them instantly to a tender medium-rare.
Top with bean sprouts, Thai basil, cilantro, and jalapeño slices. Serve immediately with a squeeze of fresh lime.