For the Cupcakes:

1. Preheat the Oven: Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with cupcake liners.
2. Mix Dry Ingredients: In a large bowl, whisk together the flour, cocoa powder, sugar, baking powder, baking soda, and salt.
3. Mix Wet Ingredients: In a separate bowl, whisk together the eggs, milk, vegetable oil, and vanilla extract.
4. Combine Wet and Dry Ingredients: Add the wet ingredients to the dry ingredients and mix until just combined. Gradually add the boiling water, mixing until the batter is smooth. The batter will be thin.
5. Fill the Cupcake Liners: Pour the batter into the prepared cupcake liners, filling each about 2/3 full. Optionally, fold in mini chocolate chips for extra chocolate flavor.
6. Bake: Bake for 18-20 minutes, or until a toothpick inserted into the center comes out clean. Allow the cupcakes to cool completely before frosting.

For the Chocolate Ganache:

1. Heat the Cream: In a small saucepan, heat the heavy cream over medium heat until it just begins to simmer.
2. Make the Ganache: Remove the cream from the heat and add the chopped semi-sweet chocolate. Stir until smooth and glossy. Let it cool slightly before filling the cupcakes.

For the Chocolate Frosting:

1. Make the Frosting: In a medium bowl, beat together the softened butter, powdered sugar, cocoa powder, and vanilla extract until smooth. Add heavy cream 1 tablespoon at a time until the desired consistency is reached.
2. Frost the Cupcakes: Once the cupcakes are cooled, use a piping bag or spatula to frost each cupcake with the chocolate frosting.

Assemble the Cupcakes:

1. Fill with Ganache: Use a small knife to cut a small hole in the center of each cupcake. Fill each hole with a teaspoon of the cooled chocolate ganache.
2. Top with Frosting: Pipe or spread the chocolate frosting on top of each filled cupcake.