Preheat the oven to 350F. Grease a 9-inch square baking pan with non-stick cooking spray. Line the pan with parchment paper, leaving an overhang for easy removal. Set the pan aside.
In a small microwave-safe bowl, combine 12 ounces of the semi-sweet chocolate chips and the butter. Melt in the microwave in 30-second cooking intervals on high heat in the, stirring in between each interval.
In a large bowl, combine the melted butter and chocolate mixture, ¾ cup sugar, and 1 teaspoon vanilla; mix until well combined.
Add the eggs one a time, stirring well until combined.
In a small bowl, whisk together the cocoa powder, cornstarch, and salt. Add the dry mixture to wet mixture and stir vigorously until the mixture is smooth, 1-2 minutes.
Fold in the 1 cup of semi-sweet chocolate chips.
Pour two-thirds of the brownie batter into the prepared pan and smooth the top with a spatula; set aside.
In a large bowl, beat the cream cheese with an electric mixer until light and fluffy. Add in the ½ cup sugar and beat until combined.
Add the egg and vanilla extract and beat until smooth.
Spoon the cheesecake mixture over the top of the brownie batter and carefully spread into a thin layer.
Spoon the remaining brownie batter over the top of the cheesecake layer.
Bake the brownies for 30-35 minutes or until a toothpick inserted into the center comes out mostly clean (you’ll see some melted chocolate from the chocolate chips, but you should not see raw brownie batter on the toothpick).
Cool the brownies completely in pan. Use the parchment paper overhang to lift the brownies out of the pan and cut into squares.