Arrange a rack in center of oven; preheat to 350°. Spray a 9" x 9" square baking dish with cooking spray and line with parchment, leaving an overhang on 2 opposite sides.
In a food processor, process cottage cheese on medium speed until smooth with no visible curds remaining. Measure out ¼ cup and reserve for brownie batter.
Add cream cheese and sugar to food processor and process until smooth, about 1 minute. Add egg and vanilla and continue to process until well combined.
In a large bowl, prepare brownie batter according to package instructions. Stir in whey powder and reserved ¼ cup cottage cheese mixture. Measure out ⅓ cup brownie batter and reserve for assembly. Transfer remaining batter to prepared pan. Top brownie batter with cottage cheese batter and spread into an even layer. Dollop spoonfuls of ⅓ cup reserved brownie batter on top. Using the pointed edge of a knife or toothpick, drag brownie mix through cottage cheese topping in figure-8 movements to create swirls.
Bake brownies until a tester comes out mostly clean with some cheesecake crumb attached, 35 to 40 minutes. The cheesecake topping will be bouncy or have a slight give in the center of the pan. Transfer to a wire rack and let cool at least 3 hours before slicing into squares.
