Preheat the oven to 350°F (175°C). Line a 9×13″ baking pan with foil and lightly spray with nonstick cooking spray.
Prepare the brownies: In a large microwave-safe bowl, melt the butter and 1 1/4 cups of chocolate chips in 30-second intervals, stirring between each, until smooth.
Stir in the cocoa powder until fully combined. Add the granulated sugar, brown sugar, vanilla, and salt, mixing until well incorporated.
Add the eggs, one at a time, stirring until each is fully mixed in. Gently fold in the flour until no streaks remain. The batter will be thick.
Spread 2/3 of the brownie batter evenly in the prepared pan. Set the remaining batter aside.
Prepare the cheesecake layer: In a separate bowl, beat the softened cream cheese and hot fudge topping until smooth and free of lumps.
Drop spoonfuls of the cheesecake mixture evenly over the brownie layer, then gently spread it out to create an even layer, being careful not to mix the layers.
Spoon the remaining brownie batter over the cheesecake layer, gently spreading it to cover. Sprinkle with mini chocolate chips or your choice of toppings.
Bake for 30-38 minutes, or until the brownies are set but still have a slight wiggle in the center. They should start pulling away from the edges of the pan.
Let the brownies cool completely, then refrigerate for at least 2 hours before slicing. Store in an airtight container in the refrigerator.