Brown the butter: Place salted butter in a light-colored saucepan over medium heat. Melt completely, then continue cooking until it foams, the foam subsides, and golden brown specks appear at the bottom. The butter will smell nutty and toasty. Immediately remove from heat and pour into a large heat-safe bowl. Cool for 15-20 minutes.
Mix base wet ingredients: To the cooled brown butter, add granulated sugar. Beat until creamy and combined, about 2-3 minutes. Add vanilla extract and eggs. Mix until smooth and glossy.
Add base dry ingredients: Add baking powder, baking soda, and salt. Mix until combined.
Divide the dough: Divide the dough into two equal halves. A kitchen scale is best for accuracy. Place one half in a separate bowl and set aside.
Make chocolate chip dough: To the dough still in the mixer, add 2 cups + 2 tablespoons all-purpose flour. Mix until just combined. Fold in 1 cup semi-sweet chocolate chips. Transfer this dough to a plate and set aside.
Make double chocolate dough: Place the reserved other half of dough back into the mixer bowl. Add 2 cups all-purpose flour and ⅓ cup unsweetened cocoa powder. Mix until fully combined. Fold in 1 cup semi-sweet chocolate chunks.
Preheat and prep: Preheat oven to 350°F (175°C). Line baking sheets with parchment paper or silpat liners.
Assemble cookies: Using a ¼ cup scoop, take one portion of chocolate chip dough and one portion of double chocolate dough. Press them together to form one large dough ball. For a marbled look, break each portion in half, rotate, and press back together. Place on prepared baking sheets, 3 inches apart.
Chill (if needed): If your kitchen is warm or dough feels soft, refrigerate assembled dough balls for 20-30 minutes before baking.
Bake: Bake for 12-14 minutes, until edges are barely golden brown and set. Centers will still look soft.
Cool: Let cookies cool on baking sheets for 10-15 minutes before transferring to a wire rack. Serve warm or at room temperature.