Grease an 8 x 8 inch square pan and line it with parchment paper. Preheat oven to 350 F.
In a medium saucepan over low heat, melt the butter and chocolate together.
Whisk in the eggs, vanilla, and sugar into the melted butter and chocolate, and beat well.
Sift the flour into the saucepan and stir well to combine. Let cool slightly. Fold in the chocolate chips.
Transfer the brownie batter to the prepared baking pan and spread it into a thin layer. Sprinkle with the sea salt. Set aside.
For the cookie dough:
In the bowl of a stand mixer using the paddle attachment, or in a large bowl using a hand mixer, beat the softened butter and sugars on high for 3-4 minutes or until light and fluffy.
Mix in the vanilla and egg, scraping down the sides of the bowl as needed to ensure that all of the batter is well combined.
Remove the bowl from the mixer and sift the dry ingredients (flour, baking soda, baking powder and salt) into the the butter mixture.
Mix on low speed to combine.Remove the bowl from the mixer and stir in the chocolate chips.
For assembly:
Use a spatula or a small cookie scoop to drop spoonfuls of the chocolate chip dough over the brownie batter. The cookie dough won't fully cover the brownie layer, and it's nice to have areas where the chocolate peeks through.
Sprinkle the remaining chocolate chips over the top (because can you ever have enough chocolate, right?).
Bake 35 minutes until the chocolate chip cookie layer is just golden brown and set.
Let cool 5 minutes. Flip the brookie onto a wire rack to fully cool, then flip back onto a cutting board. Cut in thirds vertically, and then in thirds horizontally to create 9 equal portions.
Notes
These brookies are excellent served warm, and our favorite way to enjoy them is with a scoop of ice cream! Brookies keep well wrapped in plastic wrap for several days. They've never lasted more than 48 hours in our house, so we're not entirely sure what their expiration date might be!