Place vegetable stock, onion, soy sauce, garlic, cinnamon sticks, ground ginger, star anise, and bay leaves in a large pot; bring to a boil. Reduce heat, cover, and simmer until flavors combine, 30 to 45 minutes. Remove solids with a slotted spoon and keep broth hot.
Place noodles in a large bowl and cover with boiling water. Set aside until noodles are softened, 8 to 10 minutes. Drain and rinse thoroughly. Divide noodles among 6 serving bowls.
Heat oil in a large skillet over medium-high heat until shimmering. Add tofu in a single layer and fry, in batches, until golden brown, about 6 minutes per side.
Simmer fried tofu and mushrooms in broth until heated through, about 5 minutes. Transfer to serving bowls. Top with scallions and cilantro. Ladle in hot broth.
Serve lime wedges, jalapeno peppers, bean sprouts, and basil alongside for garnishing each bowl.