In a large, heavy pot, heat the oil over medium-high. Add the onions and ginger, cut side down, and cook until browned, turning once halfway through, about 7 minutes. Add the stock, cinnamon sticks, star anise and 3 cups water; bring to a boil. Reduce the heat to medium and simmer until the onion is tender, about 15 minutes.
Strain the stock; discard the solids. Return the stock to the pot and bring to a boil. Stir in the beef and cook over medium until just cooked through, about 2 minutes. Remove from heat and stir in the noodles and fish sauce.
Divide the soup among bowls and garnish with the bean sprouts, jalapeno, basil and mint leaves.