Prep the pan.
Preheat the oven to 350°F. Grease a 9×9-inch baking dish and line it with parchment paper, leaving an overhang for easy removal.
Make the brownie batter.
In a medium saucepan, melt the butter with 1 cup of chocolate chips over medium heat, stirring constantly. Remove from heat and let cool slightly.
Transfer the mixture to a large bowl and whisk in the sugar, eggs, vanilla, and salt until smooth. Add the flour and cocoa powder, mixing just until combined. Do not overmix.
Set aside ½ cup of the batter. Stir the remaining chocolate chips into the rest of the batter and pour it into the prepared pan.
Prepare the cheesecake layer.
In a separate bowl, beat the cream cheese, sugar, egg, and vanilla until smooth and creamy. Spread evenly over the brownie layer.
Create the swirl.
Stir the hot water into the reserved brownie batter. Drop spoonfuls over the cheesecake layer and gently swirl with a toothpick or skewer.
Bake.
Bake for 35–40 minutes, until a toothpick inserted in the center comes out with moist crumbs.
Cool and slice.
Cool completely, then refrigerate for at least 2 hours before cutting into squares for clean slices.