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I do not quite understand how enemy AI works in this game. It's completely unpredictable, very easily alarmed for like no reason and seems to lock on my position no matter what I do. I'm trying to get rid of a guard in between me and a guard room but killing with the crossbow immediately alerts everyone else in the area, no matter what ammunition I use.

Can anyone explain how enemy AI works in this game, particularly in relation to stealth? Thanks.
Killing someone with any lethal weapon - even a silent one - will cause them to scream upon death, alerting any of their buddies close by. The only way to prevent them from screaming is by knocking them out instead of killing them. This can be done with the baton or riot prod.
Tranquilizer darts are generally unreliable for stealth situations. They don't knock people out instantly. The AI will fight, run, and trip alarms before finally going unconscious.

Keep your movement speed in mind. Running and jumping can be heard from a medium distance, and can be heard if an AI is a floor above or below you. Walking is much quieter, but can still be heard by the AI if you are close enough. Crouching is completely silent.

Staying crouched also reduces your visibility. The AI will not notice you as quickly as they would if you are standing up.
Most enemies seem to hear further than they can see. Never run, never walk, never jump. If you need to place something on the ground, crouch down and lower your view so that the object is placed on the ground rather than thrown or dropped. Crouching also seems to have a massive modifier making you pretty much invisible in the open whereas if you were standing or running the AI would spot you at probably 10 times the same distance.

The AI has three distinct modes of alertness also. Normally they are non-alert, just following scripted waypoints or standing around in a relaxed stance. In this stage they are very vulnerable to attacks. Melee gets a huge damage modifier against non-alert enemies. If they hear a noise or spot an enemy (including the player) they will enter a kind of alert stage where they get jumpy. They often ready their weapon while doing this. Depending on difficulty setting, noise level and distance to the player, this mode of alertness may revert back to a relaxed mode after only a few seconds ("Probably just imagining things") if nothing makes them more suspicious in this short window of time. Should the player linger a little longer in the AI's field of view they will instead enter combat mode where they will shoot you if they see you, or run around searching the area (very inefficiently and with no real logic). Explosions, gunfire and loud movement noises may also trigger combat mode even though they can not actually see the player if these things happen while the AI is already alert.

Also, enemies that are killed let out a very loud scream. Much louder than the actual sound clip may have you believe. The only noise free way of taking out enemies is to one-hit them with a baton or cattleprod from behind while they are non-alert.

What this all means is you want to crouch all the time in enemy territory. Don't break stuff, don't jump, don't run. Stay crouched near crates or angles in the geometry where you can avoid direct line of sight. Most enemies are very slow to react, you can even stick your head around a corner right in front of them and duck back without them noticing you. They all have a very limited field of view as well. If you make someone alert, just stay hidden for about five seconds and they will revert to their non-alert state and continue their scripted patrols or turn to face whatever direction they are supposed to.

The AI is very simple and easily exploited. If you are having problems you are probably breaking fundamental rules on sneaking in computer games. Deus Ex is in my opinion the EASIEST popular sneak'em'up. Deus Ex is not a shooter. There are only 2-3 characters you are forced to fight throughout the whole game, everyone else can be avoided or tricked. Don't kill anyone unless you have a clear idea what you are trying to accomplish by doing so. Even if you are sure that killing a guard makes your progress easier, do so if you can one-shot him with a melee attack or shoot him when he is isolated (by distance) with a silenced weapon while he is non-alert. AND DO THE DEED WHILE YOU ARE CROUCHED. Always crouched.