Preheat Oven: Set oven to 350°F (177°C) and line two baking sheets with parchment paper.
Prepare Dry Ingredients: In a medium bowl, whisk together flour, cocoa powder, baking soda, and salt.
Melt Chocolate and Butter: In a microwave-safe bowl, combine chopped semisweet chocolate and cubed butter. Microwave in 30-second intervals, stirring after each, until melted and smooth (approximately 90 seconds total).
Mix Wet Ingredients: In a large bowl, whisk together granulated sugar, light brown sugar, eggs, and vanilla extract for about 1 minute until well combined and slightly fluffy.
Combine Wet and Melted Mixtures: Add the melted chocolate mixture to the sugar and egg mixture, whisking until smooth.
Incorporate Dry Ingredients: Fold the dry ingredients into the wet mixture just until combined; the dough will be thick and fudgy.
Add Chocolate Chips: Let the dough rest for 5 minutes, then fold in the semisweet chocolate chips.
Scoop Dough: Using a medium cookie scoop (about 1½ inches), scoop dough balls and place them 2 inches apart on the prepared baking sheets. Optionally, press additional chocolate chips on top of each dough ball.
Bake: Bake for 10 to 11 minutes, rotating the pans halfway through, until cookies are puffed and tops are crackly.
Cool: Remove from oven and sprinkle with flaky sea salt if desired. Let cookies cool on the baking sheets for 10 minutes before transferring to a wire rack to cool completely.