In a large mixing bowl, sift the flour and cocoa powder. Add the brown sugar, granulated sugar, melted butter, orange juice or milk, eggs, orange zest, and vanilla extract, and whisk until smooth. Fold in the chopped dark chocolate or dark chocolate chunks.
Divide the cake batter between the prepared muffin cups (you should spoon about 2 tbsp/30 ml mixture into each cup). Place one muffin pan on the top rack of the oven, and another on the lower rack. Bake for 25 minutes, switching and rotating the pans halfway through, or until the tops of the cakes look just dry, which means they are barely set—this is essential to preserve their fondant texture. Transfer the pans to cooling racks and let the cakes cool completely to room temperature.
For the blood orange syrup: In a medium saucepan, bring the water, sugar, and orange liqueur to a boil. Lower the heat to medium-low, add the orange zest, and simmer until the liquid reduces to about ¾ cup (180 ml), about 30 minutes.
Strain the syrup into a measuring cup. Gently stir in the orange segments to coat with the syrup. Let cool until just warm, or room temperature, about 30 minutes.
SERVING: Serve the fondant cakes topped with a spoonful of blood orange syrup and segments.
STORAGE: Store the cooled fondant cakes in an airtight container in the refrigerator for up to 1 week, or freeze for up to 2 months. Gently rewarm the cakes before serving.
How to zest oranges: For the syrup, you can either grate the zest finely using a Microplane, or use a vegetable peeler to collect strips of zest. Make sure to leave as little white pith onto the zest as possible. Make sure to zest all the oranges before peeling and segmenting them.
How to segment oranges: First, peel the oranges. Cut off both the top and bottom of the fruit. Stand the fruit on either of the flat ends. Run a very sharp knife along the fruit from top to bottom, removing the skin and pith, leaving the flesh bare. Rotate the fruit and repeat to peel all the oranges. To collect segments, take a peeled orange in one hand, and run a sharp knife alongside the membranes, leaving entirely bare pieces of fruit behind. You should make sure to do this over a bowl and squeeze the remaining membrane to catch all dripping juices. You can add this juice to the syrup, but if you do, make sure to simmer the syrup for longer so it thickens properly. Alternatively, save the juice for your next smoothie or cocktail!
If you don’t have two muffin pans on hand, bake 12 cakes at a time. Make sure to cover and keep the remaining batter in a cool spot of your kitchen while the first batch bakes and cools. Unmold the first 12 cakes, then thoroughly wash the muffin pan. Generously coat with cooking spray, or line with parchment paper cups again, and bake the second batch as directed.
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