After the cutscene, you'll be surrounded by tank drones. Don't worry, you can call in the all-new Batmobile and take out these wave of drones.
Once cleared, bring Barbara to the Batmobile and bring her to GCPD. Once done, you have to head to the Clock Tower to stop the militia from completely messing up the server room. Also, more outposts and will become available on each island. Head to the clocktower and get to a vantage point a distance away from the building. You'll find the militia guarding the premises with snipers overlooking from the nearby buildings. Systematically eliminate them as you go, starting from the unguarded snipers.
Once you're done cleaning up, access the control console and use it to reconnect Oracle to the mainframe. After that, you'll get a new mission. (Lamb to the Slaughter)