Spray a 9-inch square baking pan with cooking spray.
Melt semi-sweet chocolate chips and butter in the microwave for one minute. Stir. Pour into a bowl. Add milk and stir to combine. Beat in eggs and vanilla until smooth.
In another bowl, stir sugar, flour and cocoa powder. Add to chocolate mixture and stir to combine. Measure out 1/4 cup of mixture and set aside for later. Spread the rest of the chocolate mixture into the prepared baking pan.
Topping
Beat cream cheese, sugar, flour, egg and milk with a mixer on medium speed until smooth.
Melt Reese's Peanut Butter Chips in the microwave for one minute. Stir together until completely melted. Pour into mixing bowl and beat on medium speed until smooth.
Pour peanut butter mixture on top of chocolate mixture in the prepared pan.
Add dollops of the reserved chocolate mixture on top of the peanut butter mixture in the pan and swirl with a knife.
Bake for 38 to 40 minutes or until set. Cool completely before serving.