Protocol 10 was devised by Hugo Strange and Ra's al Ghul to wipe out the criminal element in Arkham City, along with anyone else that could pose a threat to them by revealing the secrets about the prison - Political Prisoners. Presented to the Gotham City Council as a last resort if the inmates gained access to weapons and were planning a mass breakout, that procedure would grant the TYGER Guards full permission to exterminate the inmates with missile strikes via helicopter.
As extra insurance that major threats like the super criminals were eliminated by Protocol 10, Strange had the Observation Deck of Wonder Tower modified to hold several missile launchers. These missiles would be more powerful than the ones launched by the helicopters and were capable of taking out a large portion of a building.
After he incarcerated Bruce Wayne, Strange announced that Protocol 10 would commence within 10 hours. After he took an encryption chip from a TYGER Guard, Batman was immediately informed of the impending deadline as he progressed through the prison. He even tossed his old pawn, Quincy Sharp, into the prison, a feat that amazed the inmates as it should have been impossible to get the mayor arrested. Ensuring that his Political Prisoners would die, Strange hired the assassin, Deadshot, whom he likely kept in the dark about Protocol 10.
Strange went to City Hall, where he lied about the inmates gaining control of weapons despite his best efforts to prevent them from gaining weapons; in truth, he had given both the Penguin and The Joker various firearms to ensure that his actions of attacking the prison were justified. It was likely that Strange had kept the Mayor's arrest a secret at the time, just to ensure he could get what he wanted. Though City Hall was disappointed in him, they gave him permission anyway, unaware that Strange had imprisoned the Mayor in Arkham City.
Upon learning that Batman had broken into the Joker's hideout, Strange made it his first target. Batman and the Joker had survived the first attack (as Joker had fled earlier and Catwoman helped Batman out of the rubble). Once in full force, goons belonging to the Joker and the Penguin hid in the Sewer and Subway tunnels. Others hid by the walls of the prison. Batman downloaded the Master Control Code, infiltrated Wonder Tower and shut down Protocol 10. The only major damage suffered during the attack was suffered by the hideouts of the Joker, the Penguin and Two-Face, while the rest of Arkham City remained intact. It also appeared that the henchmen of Scarecrow were active and killed during the attack.
In Batman: Arkham Knight, it was revealed that many former Arkham City inmates had sued Gotham City Hall for giving Strange the permission to go ahead with Protocol 10 which put all their lives in danger. Those who won their court cases received a large cash payout, some up to 7 grand and were even released from prison. It's possible that supervillains like the Mad Hatter and Deadshot got their freedom that way (as the GCPD had to let them go although the reasons why were never revealed.) Gotham City Stories also implied that The Riddler got his release that way as well.
The Batman: Arkham Knight tie-in novel The Riddler's Gambit further confirms that hundreds of Arkham City inmates had died during Protocol 10.
- After Protocol 10 is done, the TYGER Guards no longer patrol Arkham City. Likely they were arrested, or left catatonic without Strange to direct them.
- The Political Prisoners managed to survive by hiding under a bridge.
- Strange mentions that Phase Two of Protocol 10 would be repeating Arkham City on both Metropolis and Keystone to wipe out the enemies of Superman and Flash.
- Throughout Knight, some thugs can be laughing that they hoped City Hall would try blowing them up again, as they needed money for their mortgages.