"A fraction of pirates camped near the church has been smuggling illegal goods into the heart of the city to the wrong people. Kill their leader."
Head to the East from the Pigeon coop you start at. You want to enter the Restricted Zone from the Southern side. There is a lift there you can easily ride to the top of the building. Deal with the patrolling guard up here then use Eagle Vision to locate your target in the courtyard below. Take him out using either a Berserk Dart or shoot using the musket from the fallen guard. Any of the buildings along the Eastern side of the area also make for an easy time of taking him out with a ranged weapon.