Preheat oven to 350 degrees.
Line the cupcake tins with paper liners.
Mix the flour, sugar, cocoa, baking soda, baking powder, and salt in a bowl.
In a separate bowl add the eggs, whole milk, oil, and vanilla.
Add the wet ingredients to the dry ingredients.
Mix all together until fully incorporated.
Beat for 3 minutes on medium.
Slowly add the boiling water.
The batter may be a little runny.
Scoop batter into cupcake paper liners until ¾ full.
Take 1 piece of cookie dough and put it in the cupcake batter. Make sure to center it and DO NOT push it to the bottom. Try to place it in the middle of the cupcake.
Bake at 350 degrees for 20-25 minutes.
Remove from oven and allow to cool for 10 minutes.
Take out of cupcake pan and place on a wire rack until completely cooled.