Preheat the oven to 350°F (175°C). Line a 9x13-inch baking pan with foil, extending over the edges for easy removal, and lightly coat with nonstick spray.
Prepare the Brownie Batter: In a large microwave-safe bowl, combine the butter and 1 1/4 cups chocolate chips. Microwave on high in 30-second bursts, stirring after each interval, until the mixture is fully melted and smooth. Blend in the cocoa powder until smooth. Add the granulated sugar, brown sugar, vanilla, and salt, stirring until fully incorporated. Add the eggs one at a time, mixing well after each addition. Gently fold in the flour until no streaks remain; the batter will be thick.
Spread two-thirds of the brownie batter evenly across the prepared pan, reserving the remaining third for later.
Prepare the Cheesecake Layer: Using a hand mixer, beat the softened cream cheese and hot fudge together in a medium bowl until smooth and lump-free. Carefully spoon the cheesecake mixture over the brownie layer in the pan, spreading gently to create an even layer.
Drop spoonfuls of the reserved brownie batter over the cheesecake layer, spreading gently to avoid blending the layers. Sprinkle with mini chocolate chips, regular chocolate chips, or chopped peanut butter cups as desired.
Bake for 30-38 minutes, until the edges begin to pull away from the pan and the center is set but slightly jiggly. Remove from the oven and allow to cool completely on a wire rack, then refrigerate for at least 2 hours before slicing.
Store leftovers in an airtight container in the refrigerator.