Preheat the oven to 350 degrees F. Spray a 9x13 pan with nonstick cooking spray and set aside.
First, make the cheesecake batter. Using an electric mixer, beat the cream cheese, sugar, egg, and vanilla together until smooth. Set aside.
In a medium-sized saucepan set over low heat, melt the butter, then add the sugar and stir to combine. Stir until mixture is shiny, but do not let it bubble or boil. Remove from heat.
Stir in the cocoa, baking powder, salt, and vanilla extract.
Stir in the eggs and stir until smooth. Add the flour and chocolate chips, stir until just combined.
Pour half of the batter into prepared pan. Place the halved truffles over the batter. Top the truffles with remaining brownie batter. Dollop the cheesecake batter over the brownie batter, then swirl in with a butter knife.
Bake the brownies for 35 minutes, or until edges are slightly puffed and center is just set. Let the brownies cool completely on a wire rack and cut into squares. I like to chill them in the refrigerator and then cut. You will cut a nice clean cut if the brownies are chilled.
Note-the brownies will keep covered in the refrigerator for up to 3 days. They are great cold or at room temperature.