Melt butter in a medium saucepan over medium heat, stirring frequently. After melting, the butter will begin to foam, then form small dark brown specks as it takes on a nutty aroma. Once the butter turns amber, immediately remove the pan from the heat. Set aside to cool for 20-30 minutes.

While the butter is cooling, preheat the oven to 350 degrees F. Line a baking sheet with parchment paper or silicone mats and set aside.

In a large bowl, whisk together the flour, baking soda, and sea salt. Set aside.

Once the butter is only slightly warm, add the brown sugar, eggs, and vanilla extract to the saucepan, and stir to combine with the butter. Pour this mixture into the bowl with the dry ingredients. Mix with a wooden spoon just until the dough comes together. Add the butterscotch chips, chocolate chips, and pretzels, and stir again to combine.

Drop large tablespoons of dough onto the prepared baking sheets approximately 2 inches apart. Bake for 10-12 minutes (10 or even less for super chewy cookies,12 if you want a bit of crunch). Allow the cookies to cool for about 5 minutes on the baking sheets before transferring to a wire rack to cool completely. Sprinkle each with a pinch of sea salt to garnish, and store in an airtight container at room temperature.