In a medium bowl, whisk together flour, sugar, cocoa powder, baking soda, baking powder, and salt. Set aside.
Heat the water in a saucepan until hot and steaming. In a small bowl, mix the buttermilk, oil, vanilla, and eggs until combined. Slowly whisk the hot water into the wet ingredients.
Using a stand or hand mixer, mix the dry ingredients for 30 seconds. Then, slowly add in the wet ingredients until just combined. Scrape the bowl and mix again for 20-30 seconds.
Use an ice cream scoop to scoop the batter on top of the graham cracker crust. It should fill up a little over 3/4 full.
Bake for 15-18 minutes until a toothpick inserted comes out clean. Let it sit in the tin for 10 minutes before transferring to a cooling rack. Allow them to cool completely. Cover and chill in the fridge for at least 1 hour or overnight before filling cupcakes.
Use a cupcake corer or a sharp knife to cut a hole in the cupcake. Only take out 3/4 of the cupcake. Don't go all the way down because the cupcake will become unstable.
Scoop all of the hot fudge into a microwave safe bowl and heat for 30 seconds. Fill the cupcakes to the top with hot fudge. The fudge should be silky and runny. If it starts to thicken, reheat it for 15 seconds.
Replace the tops of the cupcakes and store cupcakes in the fridge until marshmallow meringue is ready.