Preheat oven to 350°F.
Line a 9×9 baking pan with parchment paper, leaving a one-inch overhang on each side, and coat parchment paper with butter or non-stick spray.
In a large bowl, whisk the cocoa power, instant coffee and boiling water until smooth.
Add the chopped unsweetened chocolate and whisk until completely melted.
Whisk in the melted butter and vegetable oil until combined.
Add the eggs, egg yolks, and vanilla extract to the chocolate mixture, and continue to whisk until the batter is smooth.
Add both sugars and continuing whisking until incorporated.
Finally, add the flours and salt and mix just until combined, then fold in the chocolate chips.
Pour the brownie batter into your prepared baking pan and set aside while you make the pumpkin cheesecake layer.
Pumpkin Cheesecake Layer
In the bowl of a stand mixer, or in a large bowl with an electric hand mixer, beat together the cream cheese and sugar until light and fluffy.
Add the pumpkin puree, egg, and pumpkin pie spice, and continue beating until the mixture is completely incorporated and smooth.
Carefully spoon the pumpkin cheesecake batter over the brownie layer.
With a knife or a spoon, make decorative swirls through both batters, incorporating them slightly, until you’re satisfied with the appearance.
Bake the brownies for 35-45 minutes, or until the edges are set and the center is just barely set.
Let the brownies cool in the pan for 30 minutes, then lift then lift them out of the pan using the parchment paper as handles.
Let cool on a wire rack completely before slicing.
If desired, put these brownies into the refrigerator for about 30 minutes before slicing. It allows them to be more easily cut into neat squares.