the level that gave me the most trouble was the 'final showdown' if anyone else is stuck here then read the following. (After the cutscene that shows the scientists complaining and being killed)
I Suggest saving everytime i put a gap between parts.
Open the door, and hug the corner ready to corner grab to the right of the door on the inside. The guard automatically investigates, and you grab and do whatever you wanna do.
Continue through the rooms and hack the door, without force hack. You want to run to the left of the door, from where you were when you hacked. Now if you have some ammo you might be able to take them out, if not then equip your sound emitter and start playing about with their positions, until they've split up a bit.
Take one out while the others not looking then take the other or just run for the ladder, both tactics worked for me from the same save point.
Save before you climb the second ladder.
Some people say that you can get a smoke grenade to the ladders after the second ladder and climb up...but that means you have to pick them up. I just jumped over the edge and waited for a guard to walk on over and ten killed him, this alerts 2 or more other enemies, so i went to the back wall and went between the wall and the boxes, no one can see you here and the red-flashing light suddenly turns green.
then it's just a matter of waiting for one person to wait near you for you to get rid of, save between kills and justwait it out. if you feel that you wont be able to have enough time, make a new save slot just in case.
Once everyone's dead just scan Emile's Retina if you wish...crack the safe, hack the keypad and defuse the bomb.
Achievement unlocks at the end of this level regardless of what ending you have
*Probably add a video guide at a later date*