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This mission becomes available as soon as you reached Founder's Island. You have to neutralize the militia towers on the rooftops of the buildings in each of the districts of the city. You have to defeat all guards and place explosive gel on the console to destroy it.
Miagani Island
This is located on the rooftop of the building beside the Heavenly building. Clear the guards out of the range of the auto-turret installed on the adjacent building.
This outpost is located on top of the hospital rooftop. There are a lot of guards and there are two terminals. One of the terminals is completely unguarded. Destroy it first to disable some of the auto-turrets. Next, study the area first. There are two brutes in the fray, along with some elite guards with stun sticks.
This is found on an annex connecting two buildings in the Grand Avenue intersection. There are no guards in this watchtower, only auto-turrets. Drop down and take out the auto-turrets beside the outpost terminal.
This is found near the Mainland Bridge, NE of the Wayne Tower. There are two terminals you need to destroy. One is the unguarded terminal on the rooftop controlling the auto-turrets on the walls, and the main console on the annex with the guards. The two main towers have a lone, roaming guards. You can take them out silently to reduce the number of threats you have to deal with. Also, there is a couple of militia medics in the scene as well.
Found NE of the Orphanage, by the riverside.
This becomes available after the incident with Harley Quinn in the storyline. It's located on the rooftop of the Bank of Gotham.
This becomes available after the incident with Harley Quinn in the storyline. It's located on top of the building previously used by Penguin as a weapon cache. There's a checkpoint located beside it as well.
This becomes available only after repelling the assault in GCPD. This under the tower beside the Botanical Gardens. This is quite easy with only a drone and a handful of guards to defend the area.
Founder's Island
This is located on the rooftop of the building near the Divinity Church and bridge.
This outpost is located near Perdition Bridge and Rykes Height.
Found on the building NE of Port Adams and NW of Salvation Bridge. Use the RHD to download the security codes from the controller of the scout drone. Use the drone to take out all the guys inside instantly.
This is located south of Wayne International Plazas (which is also located near the airships). Disable their weapon caches first using the Disruptor to prevent them from arming themselves.
This watchtower is located directly north of Port Adams. The Otisburg Firestation is burning right beside it as well.
This becomes available after the incident with Harley Quinn in the storyline. It's located on top of the building in the middle of a construction. This area is not that defended so you'll have an easy way destroying these watchtowers.
TThis becomes available only after repelling the assault in GCPD. This is on top of a building under construction. There are also several mini-gunners and soldiers with sensor-deflecting armor who will appear invisible from your Detective Mode in this watchtower. You have to take out the smaller fries first then isolate the mini-gunners one by one. You can also place explosives behind the cracked walls, lure the mini-gunners there using the voice synthesizer and blow them up.
Bleake Island
The only way to enter this is by kicking through the window. Glide from a vantage point and eliminate the two guards inside to easily take out this watchtower.
This watchtower is located near the docks, north of Penitence Bridge in Founders' Island. The console is located at ground level. There are no vents that you can exploit and almost no chance for a silent takedown.
This watchtower becomes available only after Harley Quinn appears in the main story. This is located in the entrance of Chinatown. There are two drone operators here and some basic militia guards.
This becomes available only after repelling the assault in GCPD. This is found NE of the GCPD building.
This becomes available only after repelling the assault in GCPD. This is found directly north of the GCPD building. It will be hard to take this out since the auto-turret above is monitoring the position of the troops all the time. You can have the Batmobile take potshots at the soldiers that can be targeted. Unfortunately, you can't use the voice synthesizer to lure them near the edges so the Batmobile can snipe them. Once you brought down as many as you can, you have to engage them in combat. You have to work fast since the auto-turret on the wall has a rapid-fire setting. If your Batsuit's fully upgraded at this point, you should be able to take on 3-4 militia and quickly take them out via environment or special takedowns.