Preheat oven to 350F (175C) and line a metal 9x9" (23x23cm) baking pan with parchment paper, leaving enough to hang over the sides so you can easily lift the bars out of the pan once cooled (alternatively, if you plan on serving in the pan you may bake directly in a lightly greased baking pan).
Combine butter pieces and chopped chocolate in a medium-sized heatproof bowl and heat in the microwave in 25-second increments, stirring in between, until chocolate and butter are completely melted and mixture is smooth.
12 Tablespoons unsalted butter, 4 oz semisweet or dark chocolate baking bar
Add cocoa powder, sugars, eggs, vanilla, instant coffee (if using), and salt and stir until well-combined.
½ cup natural unsweetened cocoa powder, ¾ cup granulated sugar, ¾ cup light brown sugar, 2 large eggs, 1 teaspoon vanilla extract, ½ teaspoon instant coffee grounds, ½ teaspoon salt
Add flour and stir well. If using chocolate chips, stir these in now as well.
1 cup all-purpose flour, ¾ cup semisweet chocolate chips
Spread batter evenly into prepared baking dish. Transfer to 350F (175C) oven and bake for 30-35 minutes or until a toothpick inserted in the center comes out clean or with fudgy crumbs (but not wet batter).
Allow to cool before assembling, but in the meantime you can begin to prepare cookie dough topping. If you are going to be making your cookie dough topping right away, do not turn off your oven.
Cookie Dough
Preheat oven to 350F (175C) and line a cookie sheet with parchment paper.
Spread flour in an even layer over the parchment and transfer to 350F (175C) oven. Bake for 7 minutes or until temperature of flour reaches at least 160F (71C). I scoop the flour into a mound and check the temperature with an instant read thermometer. Allow flour to cool before proceeding.
1 ¼ cups all-purpose flour
In a separate bowl, use an electric mixer to beat together butter, sugars, vanilla extract and salt.
12 Tablespoons unsalted butter, 1 cup light brown sugar, ⅓ cup granulated sugar, 1 teaspoon vanilla extract, ¼ heaping teaspoon salt
Sift the cooled baked flour over the butter mixture and beat until all flour is absorbed. If the mixture is still dry and crumbly no matter how much you beat it, add 1-2 Tablespoons of milk or cream, as needed.
1-2 Tablespoons heavy cream or milk
Stir in mini chocolate chips.
¾ cup mini chocolate chips
Spread cookie dough evenly over cooled brownie layer.
Chocolate Topping
Combine chocolate chips and shortening in a heatproof bowl. Heat in the microwave in 20-25 second increments, stirring in between, until mixture is melted and cooled.
1 cup semisweet chocolate chips, 2 Tablespoons shortening
Pour over cookie dough layer and use a spatula to spread evenly.
Allow chocolate to cool until set before cutting and serving. You may transfer to the refrigerator to speed up the process, if desired.
Video
Notes
Baking pan
I use a metal baking pan. A glass dish may be used, but keep in mind that the brownie may need to bake longer.
Storing
Store in an airtight container at room temperature for up to 4 days or in an airtight container in the refrigerator for up to 10 days. Cookie dough brownies may also be frozen for several months.