Preheat the oven to 350 degrees F. Butter a 9-by-13-inch baking pan.
In a medium-large saucepan, melt the butter with the bittersweet chocolate over low heat, whisking occasionally until smooth and melted. Sprinkle in the cocoa powder and whisk to combine. Remove the pan from the heat and allow to cool for about 5 minutes.
Stir the sugar and vanilla into the chocolate mixture until just combined. One at a time, stir in the eggs. Gently stir in the flour until halfway incorporated. Add the chocolate chips and stir just until combined.
Sprinkle half of the pretzels in the bottom of the prepared baking pan. Pour the batter (it will be very thick!) in the pan over the pretzels. Spread to even out the top and arrange the remaining pretzels all over the top.
Bake for 40 minutes, then check the brownies with a toothpick. If overly gooey/messy, return the pan to the oven for 5 to 10 more minutes, being careful not to burn the edges. Allow to cool completely (important!), then cut into small squares.