MOST WANTED: Own The Roads
IMPORTANT NOTE: Make sure to purchase the Disruptor upgrade - Disruptor: Sabotage Drone for 8 upgrade points in the gadgets section. Many of the checkpoints are guarded by sentry drones which will kill you in short order if they spot you. This will allow you to destroy them without using the Batmobile.
This sidequest requires you to find the checkpoints scattered around the city and eliminate the groups of enemies (and sentry drones) inside. Each checkpoint is guarded by armed militia enemies and some are also guarded by sentry drones. Sentry drones are vicious, dealing large amounts of damage in seconds with their rapid fire guns.
They also have a large scope of vision (around 270 degrees) meaning only landing directly behind them will keep you safe from view. Sentry drones can only be destroyed with an upgraded Disruptor (see the note above) or the Batmobile. I highly reccomend getting the Disruptor upgrade as the resulting drone sentry explosion often clears the entire checkpoint of militia enemies.
The only thing that changes per checkpoint is the militia and drone numbers. One last thing to note is that nearly every checkpoint has a way for the Batmobile to access it (or at least somewhere you can fire into the checkpoint from nearby), allowing those without the Disruptor upgrade to clear them. Once the militia and drones are clear, use your detective vision to locate the checkpoint commander and interact with him to destroy his radio, opening the checkpoint walls.
Note: The custom waypoint shows the location in this screenshot