Place the onion, ginger, shallot, and garlic on top of a cookie sheet with the skin side up. Broil the vegetables in your oven for 10-15 minutes or until the outer layer of the skin is burnt.
Meanwhile, toast the spices (star anise, cinnamon, peppercorn, and fennel seeds) in a small pan over medium-high heat for 2 minutes or until fragrant. Place the spices, except for the cinnamon stick, in a tea bag or tea strainer, and set aside.
Once your vegetables and spices are ready, throw the vegetables into a large soup pot with the bone-in chicken thighs. Top the chicken and vegetables with the bone broth and water. Now add the fish sauce, honey, cinnamon stick, and the tea strainer.
Bring the broth to a boil then turn down the heat and simmer for 30 minutes. After 20 minutes, check to see if the chicken is fully cooked. If so, pull the chicken from the soup early, if not, allow the chicken to cook for another 10 minutes. Pull the chicken from the broth once cooked and allow it rest for 10 minutes then either shred it or cut it into strips. I keep simmering my broth while the meat rests.
While the broth is simmering prepare the rice noodles according to the package. Strain the noodles and rinse them in cold water. Set aside.
In a soup or ramen bowl add the rice noodles then top them with the sliced chicken, jalapeno, cilantro, basil and/or any additional ingredients you wish (like mint or bean sprouts).
Strain the broth and discard the charred vegetables (unless you can save them for something else). Ladle the hot broth over the chicken and rice noodles.
Garnish with any kind of soy, hot, or hoisin sauce you like best!