To make in the microwave In a 4-cup glass measuring cup (or similar microwave-safe container), combine the pomegranate juice, lemon juice, and sugar and microwave on high in 4-to 5-minute intervals, until the mixture has reduced to ½ cup of syrup, 20 to 25 minutes.
To make on the stove top In a 1½-or 2-quart saucepan over high heat, combine the pomegranate juice, lemon juice, and sugar and bring to a boil, stirring occasionally to dissolve the sugar. Turn the heat to medium-high to maintain a vigorous simmer or a low boil and let the liquid bubble for 25 to 30 minutes, swirling the pan now and then for even cooking, until it’s reduced by 75 percent; you should have ½ cup of syrup. (The syrup should easily coat the back of a spoon with a thickish cabernet-colored film. If you run your finger through, the line should hold; but be careful, because it’s hot.)
Regardless of your cooking method, let the hot syrup cool for 15 minutes, then transfer to a glass jar and let cool completely, uncovered, to further concentrate and thicken. Taste the molasses, and if a tart edge is needed, add more lemon juice, ½ teaspoon at a time, whisking or stirring well to combine.
Store the molasses, refrigerated, for up to 6 months. If it firms up, warm it to liquify before using.