"Your target is a Templar agent currently posing as gunner in the fort at Dry Tortuga. Find and kill him."
You must have taken over the fort Dry Tortuga. When you are ready, fast travel to the fort. Knock out the guard over the gateway with a Sleep Dart. Head through the gate and up the scaffolding in the back left. Deal with the 2 guards on the way to the scaffolding.
From the top of the scaffolding use Eagle Vision to find your target sitting on a powder reserve. Arm yourself with a pistol and blast him away.