Own the Roads

The first set of checkpoints is found in Founder's Island. The checkpoints are usually enclosed within walls so you go in and defeat all the guards. The barrier surrounding these checkpoints can't be destroyed, even with the Batmobile's cannons so you have to fly in in the middle and defeat all the guards inside. After defeating them, you have to find the commander. Enter Detective Mode to highlight the commander among those who you've beaten down and destroy the checkpoint controller to lower the barricade.

Founders' Island

1. Located directly west of Perdition Bridge
   

2. Located directly west of Penitence Bridge
   

3. In the riverside between Penitence and Salvation Bridges. This outpost has fewer men but with two armed guards and two with shock sticks.
   

4. This checkpoint is located south of Perdition Bridge, in the eastern side of Founders' Island. There are two armed guards here. Disable their weapons then engage them on the ground.
   

5. This checkpoint is inside a building compound. Pull the massive gate NW of the checkpoint using the Batmobile's Power Winch, and eliminate all guards and auto-turrets using the Batmobile's battle mode.
   

6. This becomes available after the incident with Harley Quinn in the storyline. This compound has a lot of sentry drones. It will help if you have purchased the Disruptor upgrade that will destroy the tagged drone when it fires automatically.
   

   There's also a security box that you can access to remove the barricade on the upper ground. This will allow you to bring in the Batmobile for some extra firepower.

   

7. This is found in the intersection near the abandoned church.
   

8. This checkpoint will only become available once you've rescued Oracle and got the second Batmobile. This is located inside a building on construction in the middle north part of the island. There's a drone sentry inside. Having the capability to sabotage this drone will help immensely in clearing this checkpoint. You can also sneak via underground vent this time and take them out by Fear Multi-takedown. Alternatively, there's also another switch nearby that will open the gate and allow your Batmobile to easily lay waste on them.
   
   

Miagani Island

1. This is found near Eliott Memorial Hospital.
   

2. This is found in the Urbarail Station in Bristol, east of Salvation Bridge. You can easily use the Batmobile to mow down the militia personnel stationed in this outpost.
   

3. This becomes available after the incident with Harley Quinn in the storyline. It's located beside the building previously used by Penguin as a weapon cache. There's a watchtower beside it as well.
   

4. This becomes available after the incident with Harley Quinn in the storyline. The checkpoint is located inside the compound of the Ranelagh Ferry Terminal. There are couple of checkpoint drones in the compound which you can temporarily blind using your RHD. You can only blind one at a time.

   It will be helpful to set up explosives in the lower balcony beside the station and lure the enemies there. You have to lure the checkpoint commander as well so you can get his controller. Take note that this won't disable the drones as well so get out of the area to avoid getting gunned down.

   

5. This becomes available after the incident with Harley Quinn in the storyline. It's located in front of the Orb Theater.
   

6. This checkpoint is found beside the Gotham Globe building.
   

7. This checkpoint will only become available once you've rescued Oracle and got the second Batmobile. This is located under the Botanical Gardens. Fortunately, there's a vantage point where you can snipe the drones and the guards using your Batmobile. You can even jump off the ledge and bring the Batmobile inside the checkpoint.
   

8. This is located in the upper level of the Elliott Memorial Hospital. You can also snipe them using your Batmobile from the nearby flyover.
   
   

Bleake Island

These checkpoints will only become available once you've rescued Oracle and got the second Batmobile. After finishing at least one more checkpoint, you'll get a call from Deathstroke.

1. This is found in the middle of Chinatown. There are sentry guns deployed in the entrance and the foot soldiers include most of the variety you've faced so far. There's a line hanging in the middle of the group so you can position yourself there and perform a Fear Multi-takedown. Make sure to use the disruptors too, especially on the medics and armed guards. If you have upgraded your Disruptor, you can even sabotage the stun sticks of the foot solders there. When fighting on the ground, avoid getting in the sentry guns' optical range.
   

2. This compound is located near Scarecrow's Safehouse in Chinatown. There's only one guy here surrounded by sentry guns. You can blind one of the rotating sentry guns, then disable the other while it's rotating away.
   

3. This is located near Perdition Bridge. You have to defeat the guards outside or just use your RHD to remotely hack the door switch nearby. The checkpoint commander is located inside the building. You have to enter from the side. You can conveniently perform a Fear Multi-takedown from the ledge in the side entrance as well.
   

4. This checkpoint is located near the clocktower. There are two drone sentries here but that shouldn't be a problem if you have upgraded your Disruptor that will make the drones self-destruct if they attempt to fire at you. The explosion from these drones is also powerful enough to knock down any militia near them.