Whisk the dry ingredients: In a medium bowl, whisk together the flour, cocoa powder, baking soda, and fine sea salt until well combined and no cocoa lumps remain.
Cream the butter and sugars: In a large mixing bowl, use an electric mixer to beat the softened butter, brown sugar, and granulated sugar on medium speed for about 2 minutes until light and fluffy.
Add the wet ingredients: Add the room-temperature egg and vanilla extract to the butter mixture. Beat for 1 more minute until glossy and smooth.
Combine wet and dry: Pour the dry cocoa mixture into the wet ingredients. Mix on low speed just until the dry streaks of flour disappear. Do not overmix.
Fold in the chocolate: Use a sturdy wooden spoon or rubber spatula to manually fold the semi-sweet chocolate chips into the thick dough.
Create the marshmallow swirl: Drop heavy spoonfuls of the sticky marshmallow fluff directly on top of the dough. Using a dull butter knife, gently fold and drag the fluff through the dough a few times to create thick, distinct white ribbons. Do not overmix into a gray paste.
Chill the dough: Cover the bowl tightly with plastic wrap and chill in the refrigerator for at least 30 minutes.
Prep the oven and pans: While the dough chills, preheat your oven to 350°F (175°C). Line a large baking sheet with parchment paper or a silicone baking mat.
Scoop and bake: Use a large cookie scoop to drop mounds of the chilled dough onto the prepared baking sheet, leaving about 2 inches of space between each cookie. Bake on the middle rack for 10 to 12 minutes. The marshmallow will bubble and the centers should look slightly underbaked.
Set and cool: Remove the tray from the oven. Let the soft cookies sit directly on the hot metal pan for exactly 10 minutes to finish setting before transferring them to a wire rack to cool completely.