In a small food processor or blender, pulse the ingredients for the marinade until smooth. Place the chicken thighs in a resealable plastic bag and pour the marinade over top.
Grill the jalapeno until all sides are blackened and blistering. Remove from heat, wrap in foil and allow to rest until cool enough to handle, about 15 minutes.
Stem and set the jalapeno before dicing it; Set aside. In a large pot over medium heat, add the remaining oil. Add the onion and garlic. Cook for 5 to 7 minutes.