Protocol 10

Protocol 10 is a last-resort/highest security method used to control the criminals in Arkham City by using TYGER to the destruction of many sections of Arkham City and the death of many inmates contained within.

Activation
Protocol 10 can only be activated when approved by the Gotham City Council under one scenario: if the inmates are ever able to get a hold of fire arms and appear to be attempting a mass break out. So far it appears that not many members of the council approve of this method, hoping this protocol would never be needed to have been activated. Commissioner Gordon even voiced his disgust at the measure. Bruce Wayne learned about Protocol 10 when Hugo Strange alludes to it being nearing completion shortly after Wayne ended up incarcerated. It's also implied that the protocol was virtually unknown to most of the inmates, as the Joker, when Batman asks what Protocol 10 was under the belief that Joker was in cahoots with Strange, denies any knowledge on what it is.

Batman: Arkham City
Once it was deemed that Arkham City lost its ability to control the weapons being leaked into the city (Provided by Hugo Strange), the city council approved Protocol 10. Strange devised this plan since the beginning with Ra's al Ghul to gather all of the criminals in Gotham to one place and just wipe them all out. However, Batman managed to make it to the top of Wonder Tower and stop it before the plan could be completed. However, at least 22% of the inmates were killed or injured during Protocol 10.

Trivia

 * If you search Amusement Mile during the commencement of Protocol 10, you can find dead gang members. It is rumored that these thugs work for Scarecrow's as they wear similar masks to his. What they were doing there is never explained, and their bodies disappear after Protocol 10 is shut down.
 * It would appear most of the inmates were able to survive by locking themselves in the sewers.
 * During Protocol 10, Strange voiced his plans to use Stage 2 of Protocol 10, by using Metropolis and Keystone City with prisons in a similar fashion to Arkham City. This never happened because Batman stopped Protocol 10.