2 1/4 cups all-purpose flour
1 teaspoon baking soda
1 cup (2 sticks) unsalted butter, softened
3/4 cup firmly packed light brown sugar
3/4 cup granulated sugar
3/4 teaspoon salt
2 teaspoons vanilla extract
2 large eggs
1/4 cup unsweetened alkalized (Dutch-processed) cocoa powder, sifted
12 ounces bittersweet or semisweet chocolate chips
1 1/2 cups pecan pieces

Make the cookies:

1. Position a rack in the center of the oven and preheat to 375°F. Have 2 ungreased baking sheets at hand.
2. In a medium bowl, whisk together the flour and baking soda. Set aside.
3. In the bowl of an electric mixer, using the paddle attachment, beat the butter, light brown sugar, granulated sugar, salt, and vanilla extract at medium-high speed until light, about 2 minutes. Beat in the eggs, one at a time, mixing well after each addition and scraping down the sides of the bowl as necessary. Add the flour mixture at low speed, mixing just until blended.
4. Transfer 1 3/4 cups of the dough to another bowl and set aside.
Add the cocoa powder to the remaining dough in the mixer and mix on low speed until blended. Add half of the chocolate pieces and about half of the pecan pieces and mix until blended. Stir the remaining half of the chocolate and pecan pieces into the remaining light-colored dough. Fill half of a 1 tablespoon measure with the light dough, making it well rounded, not level. Fill the remaining half with the chocolate dough. Roll the doughs into a ball and place it on an ungreased baking sheet. Flatten it into a 1 1/2-inch disc with your palm (wet it first, to prevent sticking). Repeat to form more cookies, spacing them 2 inches apart. Bake, 1 sheet at a time, for 8 to 10 minutes, until the lighter dough just begins to color. Let the cookies cool on the baking sheet for 5 minutes, then transfer the cookies to a wire rack and cool completely