Line a 9x13" pan with foil, spray with cooking spray. Preheat oven to 350 degrees.
In a large glass mixing bowl, melt the butter. Add the 1 cup of milk chocolate chips; let sit for 3-4 minutes, then whisk until melted. (If you need to microwave for a few seconds, that's fine.)
Whisk in the cocoa powder until no lumps remain, then whisk in the sugar, eggs, and vanilla.
Set aside about 1/2 cup of chocolate chips. Stir in the flour, salt, and remaining chocolate chips.
Spread batter in prepared pan. Sprinkle the reserved chocolate chips over the top.
Bake at 350° for 35-40 minutes or until the center is set. For fudgy brownies, it's better to underbake than to overbake!