Batman doesn't kill. At least he doesn't, except for those occasions when he has, but usually when tricked or mind controlled. The rule is often referenced in Batman: Arkham Knight, and the game practically bends over backwards to maintain it, especially when behind the wheel of the Batmobile, but we appreciate the effort. While most games don't mind if there's a mountain of dead bodies in your wake, there are some that allow you keep your hands relatively clean while still emphasizing the FIST in Pacifist.
Dishonored
Dishonored has two different endings that depend on the body count you leave behind. Enemies can either be knocked out or avoided altogether by skilled players. Additionally, you can choose not to kill the assassination targets by dooming them to a fate worse than death instead. However, it is very tempting to go on a murderous rampage, since the majority of powers granted to Corvo by the Outsider are spectacularly lethal. Plus, there are so many people in this world that deserve to be stabbed. We'll find out deep Emily Kaldwin's thirst for blood is when Dishonored 2 releases next year.
Deus Ex
The Deus Ex series has often prided itself on open ended decisions, like what upgrades to choose, what air vent to crawl through, and whether or not to kill everyone in sight. Human Revolution diverges from this path by forcing players into boss battles where they have choice except to kill, but there is still a "Pacifist" achievement to be had if you can stick to knocking out or avoiding everyone else. The main downside to being a pacifist is that you don't get to use cool weapons like the Typhoon, leaving you as one of the most boring advanced cyborgs around. Let's hope that Mankind Divided will help make pacifism look cooler.
Mark of the Ninja
You'd think that a game that puts you in a role of a ninja implies a lot of cutting and slicing, but that's not necessarily the case for the steal-based Mark of the Ninja. You always have the option to leave a trail of bodies in your wake, but with a bit of skill, you can sneak through the entire game without shedding a single drop of blood. Stay in the shadows, stick to the ceilings and vents, and smash lights out with your kunai for non-lethal success.
Thief
Generally speaking, Garrett is a pickpocket and burglar, but he's not a cold-blooded killer. Although, no one would blame you for firing arrows into the heads of a few guards in the fourth game. They're just so unsuspecting and tempting. However, the game's scoring system encourages you to slip in and out without confronting anyone. You even have to option to ditch out of boss battles. If you simply can't resist a little bit of violence, you could use your trusty blackjack to knock people out. However, the pacifism route doesn't apply to the first two games, since there are main bosses in desperate need of killing, but Garrett manages to eliminate them indirectly, which is sort of a roundabout way of keeping a clear conscience.
Mirror's Edge
Faith is a messenger, not a killer... unless she wants to be. It's very easy to use her martial arts skills to disable guards, steal their weapons, and use them against other enemies. However, avoiding firearms will get you the "Test of Faith" achievement, and the satisfaction of taking the high road. We'll see how tempting it will be to start shooting when Mirror's Edge Catalyst releases on February 23rd, especially with the refined combat system.
Perfect Dark
As highly skilled spy working during an interstellar war, players always have the option to kill everyone in their path. In fact, they're given a multitude of tools to accomplish that very goal, but they don't have to. Perfect Dark gives players the option to disarm enemies instead of killing them. The majority of disarmed enemies will simply give up, but there are a few that will pull out a secondary weapon or use their fists. At that point, you can knock them unconscious with a punch or by pistol whipping them. Fans will have a chance to test their Perfect Dark pacifism skills when the Rare Replay collection releases on August 4th.
Fallout 3
The Fallout games often pride themselves on having a broad range of open-ended choice, and that includes not killing anyone while wandering the insanely dangerous wasteland. With the exception of shooting a radroach in the tutorial, you can complete Fallout 3's main story and a good number of side quest without directly killing a single living creature. So, all those mutants, ghouls and giant insects can rest easy, because their head won't explode anytime soon. However, it's an extremely difficult feat to accomplish, and you may still be indirectly responsible for the deaths of many. Also, the no kill rule does not apply to New Vegas, since all four its endings require that least one person be killed. We'll see whether players can survive without killing in Fallout 4 when it releases in the fall.
Almost: Infamous: Second Son
It almost possible to play through all of Infamous: Second Son by subduing everyone in your path instead of killing them with your incredibly lethal powers. However, there is a part of the game where Delsin Rowe becomes so enraged that subduing enemies no longer becomes an option. But hey, points for trying.
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Steven Wong posted a new article, Thou Shall Not Kill (But Beatings Are Fine): 7 Games for the Violent Pacifist