You will find him first across and to the left (south) of the GCPD building. He will talk to you and leave a symbol on the ground. Scan it.
You will also meet him on top of one of the buildings south of the courthouse. Look out from the courthouse steps and the building across the street to the right. He should be on the corner closest to you.
You can also find him on top of the Ferris wheel in the Industrial District. It's in the eastern part of the district, by the water. Climb up and talk to him.
You can also find him Northeast of Catwoman in the Bowery. He will be on the NW corner of the building and he will leave another symbol on the ground. After this, the map will open up and Batman will notice that the symbols line up. The answer to this puzzle is as follows:
You should have 5 circles. There are three very close together and they should be toward the top of the map. Four of the circles will be points where you met the watcher. The top middle circle will be on the right side of the Church, upper left will be south of the courthouse, upper right will be just west of the GCPD, lower left will be just north of the subway entrance in the Bowery and the bottom right will be just north of the east side of the Steel Mill. This will reveal the 5th spot by the church. Go there and then if you look NW then you should see the last symbol on the wall. Scan it.
Note that the Watcher may not appear until you finish the story line for this section.