Preheat oven to 350F. Line an 8X8 baking pan with parchment and set aside.
Set a pot of water to boil and place a bowl on top. Add chocolate and butter, stirring until fully melted. Remove from heat and let cool to room temperature. Stir in molasses.
Combine eggs, sugar, and vanilla extract. Whip with a hand mixer or stand mixer until thick and light in color.
Add a small amount of the chocolate mixture to the egg mixture and mix it. Add into egg mixture with remaining chocolate mixture. Fold gently until incorporated.
Sift in flour and cocoa powder. Fold gently with a rubber spatula until combined.
Pour brownie batter into the baking pan, reserving 3/4 cup on the side.
In a separate bowl beat cream cheese until smooth. Add vanilla and egg yolk and beat until combined, being sure to scrape the sides down.
Alternate spoonful's of cream cheese mixture and brownie batter so you get a checkerboard pattern. Use a butter knife to create a swirl pattern, being careful not to overdo it. Less is better here so the swirl pattern remains defined.
Bake for 30 minutes, until edges begin to turn golden brown. It's okay if a toothpick inserted in the center comes out with a little brownie batter on it.
Cool completely first and refrigerate for at least 2 hours before cutting.