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In my first playthrough, I was able to get out of the ship without setting off the alarm. In my second playthrough, despite knocking out every guard and never triggering an alarm, when I passed the security checkpoint I was notified that the base was put on an heightened alert state due to some alarms from the ship. What did I do differently? The only thing I remember is a turret seeing me for a few seconds.

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IIRC, any turret sightings count as an alarm, even if it doesn't set off the rest of the guards. –  Jeff Mercado Apr 5 '12 at 3:57
    
@JeffMercado hmm... the weird thing is I got ghost and smooth operator on all the missions –  z - Apr 5 '12 at 11:07
    
Funny, when I reached the first mission with the turret, I remember not getting those bonuses because I tried to be cute and just jump past the hall. Fortunately I saved beforehand and reloaded and dispatched of the turret and got those bonuses. It might have changed since then with all the patches. –  Jeff Mercado Apr 5 '12 at 16:23
    
Also, if a turret or camera spots a dead/unconscious body, it will usually trigger and alarm. –  Phill.Zitt Jul 26 '12 at 23:46
    
Yesterday I tried the Factory Zero achievement and though I failed (whyever?) the base wasn't alarmed. Now I entered it and saw the huge amount of soldiers and the robot that was never active during my first playthrough... i am so annoyed by this and have to go back a few savegames to try out where I failed... did you actually find out, what you did wrong? –  Christian Ivicevic Sep 25 '12 at 12:34
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