I have played through the main storyline of Arkham City, and somewhere along the course of the game I missed the mission for the Mystery Watcher. According to this website, he still spawns after the main missions are over, but is that really the case, and if so, does anyone know where I need to go to find him?
Once you have all 4 sigils:
Scanning the fourth symbol that the watcher leaves behind will automatically take you to the Batcomputer screen. Use the right and left sticks to rotate and move the sigil so that its four points match the four locations in which you spotted the watcher. Doing so reveals the watchers final location: the eastern side of the church. Scan the symbol on the wall there to complete this side mission.