Step 1: Prepare the Blackberry Filling

1. In a small saucepan, combine 1 cup fresh blackberries, 2 tbsp granulated sugar, and 1 tbsp lemon juice.
2. Cook over medium heat for 5-7 minutes, stirring occasionally until the blackberries break down and form a syrupy mixture.
3. Remove from heat and set aside to cool.

Step 2: Prepare the Cupcake Batter

1. Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with cupcake liners.
2. In a medium bowl, sift together flour, cocoa powder, baking soda, baking powder, and salt.
3. In a large bowl, cream together butter, granulated sugar, and brown sugar until light and fluffy (about 3-4 minutes).
4. Add the eggs, one at a time, beating well after each addition. Stir in vanilla extract.
5. Gradually add the dry ingredients into the wet ingredients, alternating with milk. Mix until just combined.
6. Gently fold in fresh blackberries until evenly distributed.

Step 3: Fill the Cupcake Liners

1. Fill each cupcake liner about 2/3 full with the batter.
2. Add 1 tbsp of cooled blackberry filling into the center of each cupcake. Gently push it down into the batter using a small spoon.
3. Bake for 18-22 minutes, or until a toothpick inserted into the center comes out clean or with a few moist crumbs. Let the cupcakes cool completely on a wire rack.

Step 4: Make the Chocolate Ganache Frosting

1. Chop dark chocolate into small pieces and place in a heatproof bowl.
2. In a small saucepan, bring heavy cream to a simmer over medium heat.
3. Pour the hot cream over the chopped chocolate and let it sit for 1 minute. Stir until smooth and glossy.
4. Stir in butter until fully incorporated.
5. Let the ganache cool for 15-20 minutes, or until it reaches a spreadable consistency.

Step 5: Frost the Cupcakes

1. Once the cupcakes are completely cooled, frost them with the ganache using a piping bag or a spatula.
2. Garnish each cupcake with a few fresh blackberries for decoration.