Preheat your oven to 350 degrees F. Line a 9x13 inch baking pan with parchment paper, leaving a couple inches of overhang on the long sides so you can lift the brownies out later. Lightly grease the parchment.

Make the brownie batter. Melt the butter in a medium saucepan over low heat, then remove from heat and stir in the 1 1/4 cups sugar. Let it cool for 5 minutes. Whisk in 2 eggs and 1 teaspoon vanilla until smooth and glossy. Add the flour, cocoa powder, salt, and baking powder and stir with a spatula until just combined. Fold in chocolate chips if using. Spread the batter evenly in the prepared pan, using the back of a spoon to push it all the way into the corners.

Make the pumpkin cream cheese filling. In a medium bowl, beat the room-temperature cream cheese with a hand mixer on medium until completely smooth, about 1 minute. Add the pumpkin puree, 1/4 cup sugar, remaining egg, remaining 1 teaspoon vanilla, cinnamon, ginger, and cloves. Beat until smooth and creamy with no lumps. If your cream cheese was cold, the filling will have small lumps and the swirl will not look clean, so room temperature is important here.

Add the swirl. Drop large spoonfuls of the pumpkin cream cheese mixture all over the top of the brownie batter, spacing them out fairly evenly. Use about 8 to 10 dollops. Drag a thin knife or skewer through the batter in long, lazy S-curves and figure eights. Do not over-swirl or the two layers will blend together and lose the marble look. About 8 to 10 strokes is plenty.

Bake for 30 to 35 minutes. The edges should look set and the cream cheese layer should no longer look wet and shiny. The center can have a very slight jiggle when you gently shake the pan, like a cheesecake. A toothpick inserted in the brownie portion should come out with just a few moist crumbs, not wet batter.

Cool completely in the pan on a wire rack. This takes at least 1 hour at room temperature. For clean, even cuts, transfer the pan to the refrigerator and chill for an additional 1 hour before lifting out by the parchment and slicing into 16 bars. A warm knife wiped clean between cuts gives the sharpest edges.