Place the bacon in a large skillet and cook over medium-high heat, turning occasionally, until evenly browned, about 10 minutes. Drain the bacon slices on paper towels.
Mix flour, cocoa powder, and baking soda together in a bowl.
Beat butter, brown sugar, and white sugar together with an electric mixer in a large bowl until smooth. Beat 1 egg into butter mixture. Beat second egg into mixture along with the vanilla extract; add flour mixture and mix well into a cookie dough. Crumble bacon and add to the dough with the chopped peanut butter cups; fold bacon and peanut butter cup chunks through the dough. Drop peanut butter in small amounts into the dough and swirl into the dough, but not mixing completely to integrate.
Drop spoonfuls of dough onto baking sheets.
Bake in the preheated oven until the edges are golden, about 12 minutes.