In a medium bowl, combine flour, baking soda, and salt. Whisk until fully combined; to aerate.
Melt butter completely in a microwave safe bowl. In a large bowl using an electric mixer, cream together the brown sugar, white sugar, and melted butter. Beat in the vanilla and eggs. Continue beating until batter is light and creamy. In increments, add in flour mixture, mixing after each addition.
In a small bowl, crush 1 cup of the Cap'n Crunch with a potato masher. If you do not have a potato masher, put the Cap'n Crunch into a small zip lock bag and smash. Add crushed Cap'n Crunch to the dough mix, stirring by hand. Then add in the other cup of non-crushed Cap'n Crunch and mix well by hand.
Place 1" balls of dough on cookie sheet lined with parchment paper. Bake 8 to 10 minutes until edges are a light golden brown. Remove from sheet to cooling rack.