Far Cry 3 Blood Dragon

There are 13 garrisons spread out across the map. When looking at the big map, unliberated garrisons look like hexagons with a red center, while liberated garrisons have a green center.

It is best to sneak into a garrison and disable the alarms by pressing (X) on a pole with 4 speakers on top. That way, reinforcements can not be called if your cover is blown, making the fighting much more easier. Disabling one alarm with (X) disables all the alarms for that garrison. It is also possible to disarm the alarms from a far with a silenced weapon, but you have to disable each alarm for that garrison if there are multiple alarms.

Other ways to liberate a garrison include blowing up shield generators, shutting the shields off with a button, throwing cyber hearts at the base and luring blood dragons to do your dirty work, or just go in with guns blazing.

All of the garrisons can be liberated before the story is over if you take time to explore the island instead of going straight for the story missions. However, you are free to explore the island and liberate garrisons after the main story is over.