Recipe adapted from John Barricelli, owner, SoNo Baking Company and Cafe, Norwalk, Westport, and Darien, Connecticut, and cookbook author.
Preheat oven to 350 degrees, with racks in upper and lower thirds. Line two baking sheets with parchment paper. In a medium bowl, whisk together flour, salt, pepper, and baking soda; set aside.
Place unsweetened chocolate, 1 cup semisweet chips, and butter in a medium heatproof bowl set over (not in) a pan of simmering water. Cook until chocolate begins to melt, about 5 minutes. Stir until chocolate is completely melted and mixture is smooth. Remove from heat and let cool 3 minutes.
Add sugars and, with a rubber spatula, stir until sugars dissolve, about 4 minutes. Add eggs, one at a time, stirring well after each addition. Stir in vanilla. With spatula, fold in flour mixture just until flour is absorbed. Fold in remaining semisweet chocolate chips.
Scoop dough by level 1/4-cupfuls onto baking sheets, 3 inches apart. Bake until cookies are set at edges but still soft in center, 11 minutes (do not overbake), rotating sheets halfway through.
Let cookies cool on sheets on wire racks, 10 minutes, then transfer to racks to cool completely, 30 minutes. (Store cookies in an airtight container, up to 2 days.)