Preheat the oven to 350 degrees F. Spray a 9x13-inch baking dish with nonstick spray.
For the brownies, add the butter and chopped chocolate to a microwave-safe bowl and microwave until melted, 30-60 seconds. Once the chocolate is semi-melted, stir constantly to melt the rest. Set aside and allow the mixture to cool for 5 minutes.
In a small bowl, whisk together the flour, cocoa powder, baking soda, baking powder, and salt.
In a large bowl, whisk together the melted butter-chocolate mixture and granulated sugar. Whisk in the eggs, egg yolk, and vanilla extract, stirring until a smooth batter forms. With a large spoon, mix in the dry ingredients until combined. Stir in the chocolate chips. Add the batter to the baking dish. Bake until the brownies are set and no longer jiggly in the middle, 25-30 minutes. Remove from the oven and let them cool for 30 minutes.
For the peanut butter filling, stir together the melted peanut butter, powdered sugar, and coconut oil until smooth. The peanut butter will be warm and will melt the coconut oil, so stir until melted. Pour the filling over the brownies, using a spatula to spread it around the top. Let cool completely and firm up, about 20 minutes.
For the ganache, add the chocolate to a large bowl. Heat the cream in a small saucepan over medium heat just until it bubbles around the edges. Remove the cream from the heat and pour it over the chocolate. Let the mixture stand for 30 seconds, then stir until the chocolate melts and a smooth ganache comes together, about 1-2 minutes. Pour it over the top of the brownies, then cover with the chopped peanut butter cups. Let the brownies sit for 30 minutes before cutting.
Note-the brownies will stay fresh for 2 to 3 days at room temperature if covered or kept in an airtight container. You can also keep them in the fridge, they will last a few days longer.