File:Unconscious.png|thumb|An unconscious NSF terrorist, note the lack of blood on the ground. Also shown is a riot prod, used to KO enemies.
In Deus Ex, the player has the option to not kill NPCs, either by merely "knocking out" hostiles with certain weapons or just avoiding them entirely. Some people choose to do entire walkthroughs of the game without killing enemies, usually called "non-lethal runs" or "pacifist runs". In the normal game, pacifistic runs have almost no benefit to the player, except for when fighting NSF on Liberty Island and when encountering MiBs. If the player kills several terrorists in the early part of the game, Paul will react negatively and Sam Carter won't give the player the extra ammo he would give otherwise. MiBs and WiBs usually explode on death, destroying their inventory, but if they are knocked out then they can still be looted. Knocking out important characters may lead to them returning later in the game; if the player chooses to avoid or incapacitate Walton Simons in the Sub Base he will return in Area 51, but if the player incapacitates Gunther Hermann in Paris he will not reappear again in the game.
NPCs can be eliminated like this from a few weapons. First, the Baton (DX)|Baton is a reliable choice if nothing else is present. It is rather weak, but enough hits from it will knock out opponents and it does not use any ammo, unlike the more powerful riot prod. The Riot Prod will momentarily freeze enemies, but they will wake after a moment. If they are hit a second time, or once if hit from behind/in the head, they wil be knocked out for good. The prod always works the same way on all humanoid enemies, including MJ12 commandos and greasels. Tranq darts on the Mini-crossbow allow non lethal takedowns from a distance, but it will still alert nearby enemies, and the target may reach an alarm before the drugs take full effect. ''One must remember that, although they are melee weapons, the crowbar, knife, sword, and DTS all kill people.'' The Pepper Gun|pepper gun and gas grenades do not kill people, but they will not KO people either. They are best used to stop enemies long enough for the player to complete the objective, escape, or even kill active NPCs if they are doing a lethal run. If they are having trouble taking out tougher opponents, one can always inflict damage with lethal weapons, and if they deliver the "killing" blow with a baton or tranquilizer dart, it '''wont''' count as a kill.
Different people may have different rules. Some people may still consider it nonlethal so long as ''they'' don't kill the NPC directly, such as leading a bot to enemies or leading enemies to friendly NPCs. Others may not even attack enemies, solely using stealth. While the game scripts certain unavoidable encounters, such as the fights with Anna Navarre and Gunther Hermann, certain exploits may allow the player to get around them.
The Shifter Mod adds a more in-depth skill point system, where the player gains more points for not killing enemies.
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