Stealth Run

In Stealth Based Games, the player is usually not required to be stealthy all the time. One will often be able to escape or kill opponents that discover the player character at an opportune moment. A Stealth Run an attempt to play through one of these games without being discovered at all, and some games actually reward such behaviour.

An even harder version of the Stealth Run is the Ghost Run. Mixing the Pacifist Run with the Stealth Run, the player tries to play through the game without being noticed by or taking down a single enemy, unless the plot calls for it.

Do not confuse with Stealth Pun.

Action Game

 * Final Ninja 1 and Prequel give an end-of-level point bonus for not being seen. The latter makes it a bit harder to get this bonus, though--the bonus for a Pacifist Run is replaced by one you get if you Leave No Survivors, and killing people is one of your primary ways of scoring points, so unless you're a truly sneaky or truly pacifistic fellow you'll probably forfeit the stealth bonus while getting the kill bonus.

First Person Shooter

 * Pacifist runs are possible in many levels throughout the Jedi Knight series of games, popular amongst some enthusiasts who enjoy following the Jedi Way, especially once one attains the ability to disarm or to mind trick their way through the countless hostiles. Averted in some levels thanks to a stated mission objective. Clearing a level is also an unstated event trigger late in Jedi Outcast. Ergo, a disarm-only approach can require very un-Jedi-like measures to proceed.
 * While the game as a whole doesn't encourage it, especially with the need to kill some teams of bandits or mutants, Metro 2033 rewards you with achievements and Morality Points for doing some of the more challenging 'war' missions without being seen or killing anyone.
 * In Medal of Honor: Frontline's Operation Repunzel level, the guard at the entrance usually notices you and blows your cover, but if you're lucky, you might sneak past him. Similarly, you can stealth run On Track via a Good Bad Bug. These don't work in the PS3-exclusive remaster, however.
 * Deus Ex Human Revolution may not be a fully Stealth-Based game like the entries further down, but it does award big XP bonuses for completing objectives without being spotted and without setting off any alarms, sometimes more than you might earn for using a non-lethal takedown on every Mook between you and the objective. With skill and patience, it is entirely possible to do a full Stealth Run through almost all mission environments. They're even called Ghost (avoiding detection) and Smooth Operator (avoiding alarms).

MMORPGs

 * If playing solo in Final Fantasy XI, if you need to go in a dungeon with enemies that aggro, you get shoved into a Stealth Run, as if you do get aggro, you either fight a single enemy for too long and get his buddies on you, or you get the attention of something that can kill you in 2 hits. Gets increasingly hilarious/frustrating when you sometimes have entire parties have to go through a Stealth Run. Not pretty.
 * Rogues and Druids in World of Warcraft have literal Stealth abilities, and players of these classes often try to Stealthrun certain parts of instances, avoiding rather pointless fights to finish the run faster. Since Druids are jacks-of-all-trades, this tends to work well... except for the expansion, who made this considerably harder with stealth-detecting enemies.
 * Stalkers are best at it, but all characters in City of Heroes can pick up stealth skills. While most of the really rewarding arcs involve fighting things, you will often come across missions that only require you to pick up a single object at the end of a gauntlet of enemies.
 * Similarly in Dungeons and Dragons Online, anyone can learn the skills required but wizards tend to be surprisingly good for stealth runs as they, unlike rogues whose backstabbing abilities don't work when fighting alone, pack the necessary punch to defeat the end boss. There is also a low-level quest where this is all but required if one wants to avoid being chased by hordes of mooks, a certain type of which (very conveniently the ones among the easiest to kill) mustn't be killed or the quest will fail.

Platform Game

 * Metroid Zero Mission has a section where Samus is without her famous suit. Depending on the player's skills, this is either a long chase section, or a stealth section. There's no real reward for getting through undetected though, aside from not being shot at. That, and being able to listen to the cool music, rather than the sort of lame music.

Role Playing Game

 * The Thieves' Guild quests in The Elder Scrolls Oblivion can be ghosted except for three creatures: two vampires who must be killed, and a monster fish that is impossible to sneak past.
 * Mass Effect 2 - Infiltrating the prison and finding Kenson during the Arrival mission without alerting any guards earns you the Covert Action achievement.

Simulation Game

 * Stealth Run was an option in Sid Meier's F-19: Stealth Fighter. Guess why. You were supposed to destroy the planes and radars you were detected by, and your mission objective.

Stealth Based Game

 * Popular among the Thief community, where it is usually referred to as "ghosting". This usually involves not being discovered at all, not killing or knocking out any NPCs, not leaving any doors or chests open and not disturbing any objects that are not lootable valuables. On the harder difficulty levels, this is enforced (though usually they draw the line at "Don't get spotted, don't kill or knock out anybody").
 * The Hitman series has several titles that can be given to the player after a level. The greatest of these, "Silent Assassin", requires you to perform a Stealth Run - you cannot be seen, must not kill anyone other than the target(s), and are allowed only one shot from a silenced weapon per target. Variations of stealth run include the "Suit-Only" Silent Assassin run (where you're not allowed to change your outfit during the course of the mission), and - in Hitman: Blood Money, "All Accidents" (where all of your kills have to be listed as being "accidents", natch).
 * In the Metal Gear series, a stealth run is defined as low/no Alerts, while alerting an enemy to your presence without being seen doesn't count against you, and is often the only way to get through certain areas undetected. Naturally the series rewards you for being stealthy:
 * Metal Gear Solid 3 allowed you to unlock the Stealth Camo by going through the game without getting seen at any time. Since the Stealth Camo rendered you invisible, a cheat of a bonus in a Stealth Based Game, it was a very notorious case of the fact that the player good enough to win the Game Breaker doesn't need it.
 * You get the Stealth Camo in Metal Gear Solid 4 either by coughing up an outrageous amount of in-game currency or by clearing the game without causing any alerts. Of course, Unmanned craft like the Gekko can still see you with it equipped and there's at least one optional "emblem" that requires you to use no special items (Of which the Stealth Camo is one) and still get no alerts.
 * These games also have an extra play mode on harder difficulties where the game ends immediately if the player is discovered, which pretty much forces players to do a Stealth Run through the whole game.
 * Starting with Metal Gear Solid 4, the series has avoided making mandatory alerts through story-required Inescapable Ambush by initially placing the ambushing enemies in Caution Mode, i.e. on high alert without knowing exactly where you are.
 * In Peace Walker the game outright cheats in your favour by disabling Alerts entirely during the action-packed mission "Get to the Control Tower".
 * Tenchu series:
 * Scoring in Tenchu 2 is based on the number of enemies killed, with penalties for being spotted or killing a bystander. There's no Pacifist Run here, kids; a stealth run in this game thus consists of killing every enemy in a level without being spotted once.
 * Tenchu 1 and 3 give you an initial 300 points and a bonus 150 for not getting seen. It's possible to get the highest rank, Grandmaster, without killing anybody, except level bosses.
 * The Splinter Cell series has caught on slowly to the fact that many fans of the series like to attempt stealth runs; by the third game, Chaos Theory, they gave statistical breakdowns of how stealthy you had been in each mission (how many times you were spotted, how many guards you had to knock out, etc), then in the fourth, Double Agent, you unlocked additional items if you performed above a certain level of stealth -- oddly, these items were mostly new types of grenades, weapon upgrades, all manner of things which are only useful if you don't want to use stealth.
 * Assassin's Creed Brotherhood encourages this with its Perfect Assassin objectives, optional goals for missions that typically manifest as "Complete the mission without being detected". However, the game only cares about the player: you can call in the Brotherhood to slaughter everyone in a riot of smoke bombs and high-profile kills, and still have it counted as a stealth run so long as Ezio stays out of sight.