There are a total of 16 ctOS Breaches in Watch Dogs. Completing all of them will earn you the System Mangler Trophy / Achievement.

To unlock their locations you must activate all 13 ctOS towers. The ctOS Breaches are little side events in which you must hack 5 boxes within a certain time limit. You often have to climb up buildings or use surveillance cameras to reach them. In some cases you even need to place a vehicle in front of a wall and use it as a stair. You can start the breaches by hacking the first box.

As with all other side activities and collectibles you can still do this after beating the story.

TIMELINE:
#1 - Parker Square - 0:05
#2 - Parker Square - 1:38
#3 - Parker Square - 4:08
#4 - Parker Square - 5:46
#5 - Mad Mile - 6:58
#6 - Mad Mile - 8:48
#7 - Mad Mile - 11:12
#8 - The Loop - 13:38
#9 - The Loop - 15:21
#10 - The Loop - 16:59
#11 - Brandon Docks - 19:17
#12 - Brandon Docks - 21:58
#13 - Brandon Docks - 24:44
#14 - Brandon Docks - 27:09
#15 - Brandon Docks - 29:06
#16 - The Wards - 31:32