Preheat oven to 400 degrees.
Cut apples and jalapeños in half. Remove apple cores. Remove as much of the jalapeño seeds and ribs as desired (leave more in for more heat). Place on a sheet pan lined with parchment paper or a silicone mat and bake at 400 degrees until skins darken and blister.
3 apples, cored, 4 jalapeños
Peel skins from the apples and jalapeños, then add to the saucepan with the bourbon and heat until simmering. Simmer 10 minutes.
1 cup bourbon
Remove the apples and jalapeños to a food processor (it's okay if some bourbon goes with it) and process until smooth, then add back to the saucepan and bring back to a simmer.
In a separate bowl, whisk the ketchup, tomato paste, liquid smoke, and molasses until well blended. Add this mixture to the saucepan with the bourbon mixture and whisk until blended. Simmer an additional 20 minutes.
1/3 cup apple cider vinegar, 2 cups ketchup, 1 6 oz can tomato paste, 2 tbsp liquid smoke, 2 tbsp molasses
Remove from heat and cool until it can be stored in a container or squeeze bottle and refrigerate.