Preheat Oven: Preheat oven to 325 degrees (F). Line two large baking sheets with parchment paper, lightly spray them with non-stick spray and set aside.
Prepare Dry Ingredients: In a medium bowl, whisk together the flour, cocoa powder, baking powder, and salt set aside.
Melt Chocolate and Butter: In a large, microwave-safe bowl, combine one cup of the chocolate chips and the butter. Heat them in the microwave, on low power, in 15-second increments, mixing in between each, until butter and chocolate are completely melted and can easily be whisked smooth.
Mix Wet Ingredients: In a large bowl, whisk together both sugars and the eggs, beating until well combined. Beat in milk and vanilla. Then fold in the melted chocolate, stirring until evenly combined.
Combine Wet and Dry Ingredients: Using a rubber spatula, fold the dry ingredients into the wet ingredients, stirring just until combined. Do not over mix here!
Add Remaining Chocolate Chips: Fold in the remaining chocolate chips, stirring until everything is just combined.
Scoop Batter onto Baking Sheets: Scoop 1/4 cupful of the batter directly onto the prepared baking sheets, leaving room for spreading.
Bake: Bake, one tray at a time, for 15 minutes, or until the edges are set and the tops are dark and shiny.
Add Toppings: Press a few extra chocolate chunks on top of the warm cookies and sprinkle with sea salt.
Cool: Allow cookies to completely cool on the baking sheet for one hour before serving.