Put the butter in the medium sauce pan and heat over medium low heat. Watch carefully. Swirl the butter gently and watch for browning. You will see small browned milk fats forming and the liquid will become golden. It will foam as the water evaporates out. Stirring or swirling allows you to watch for the color change and make sure it doesn't burn. Once the butter has browned, set aside to cool for 5 minutes.
Into the saucepan with the brown butter, add the brown sugar, molasses, and vanilla extract and whisk vigorously. Then add the 2 eggs and whisk again for a few minutes until the mixture changes to a slightly lighter color. This is how you are adding some air into the mixture.
In the large mixing bowl, add the flour and baking soda. Mix the dry ingredients together then add the wet into the dry and mix until mostly incorporated.
Chop the chocolate bars into small chunks and then add all the chocolate into the cookie dough and fold in until the chocolate is well distributed and there is no visible flour in the mixture. Set aside while you preheat the oven.
Preheat the oven to 350 F.
Line the sheet tray or sheet trays with a silicone mat or parchment. Portion the cookie dough into 2 inch balls. I like to use an ice cream scooper to portion each ball and make sure each cookie is the same size. Arrange them about 3 inches apart and bake for 12 minutes.
After 12 minutes, remove the cookies from the oven, sprinkle the tops with flaky salt and allow to cool on the sheet tray for 2-3 minutes before transferring to a cooling rack.
This recipe makes 30 cookies. You can portion all the balls and then store them in the freezer or fridge and bake off just a few at a time. Just allow the frozen balls to thaw before baking. Don't skip the flaky salt. There is not salt in the recipe other than the salted butter so you will want a little salt on top to balance the sugar and dark chocolate.