Story Related.
You DO NOT have to play the game all over again, to get any of the ending achievements. Just click continue.
For speeds sake, do this ending last, it is also the only good ending.
End game, after you fix the computer to deal with the supercomputer, turn it off, then another terminal will open on the other side of the room, choose to open the cage will free the GenSec giving you this achievement and the good ending.