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It's been said by many critics that stealth is essentially broken in Alpha Protocol but that's not really true. The stealth system is definitely not as well fleshed out as in some games, nor is stealth nearly as obvious. For example, there is no meter to tell you when you're hidden, and hiding in the shadows doesn't guarantee you'll not be seen. But the developer did go to great lengths to give you the tools you need to make Agent Thorton stealthy. It just takes some time and effort on your part to learn the best way to do it.

First of all there are skills you'll want to use if you choose to use stealth to make it through the game. You will want to put most of your points into the Stealth skill but you can also focus on Pistols and Martial Arts. These three skills are the basis of the Spy specialization in Alpha Protocol, and they allow you to avoid detection, fire tranquilizer darts, as well as silently engage enemies.

Pumping points into Stealth gives you essential skills such as Awareness, which tells you where enemies are located, their facing, and their current status. Evasion lets you show yourself to the enemy briefly without them actually seeing you. Silent Running allows you to move silently. And there are a couple of other skills, as well as various levels of the ones I've already mentioned, that further make you hard to detect.

Pumping points into Pistols allows you to to more accurately use tranquilizer ammo to sedate enemies without killing them. I don't think it's quite as necessary to put a lot of points into Pistols but there are a few skills, such as Chain Shot, which can come in handy.  Furthermore, the more proficient you become with a pistol, the more able you are to get critical hits against enemies.

Pumping points into Martial Arts increases your offensive and defensive melee abilities.  While Martial Arts is quieter than shooting a firearm at an enemy, you are still killing them when you beat them to death, so it's actually more important to sneak up on enemies and use the non-lethal take down to neutralize them if you want to avoid kills. But having the ability to protect yourself as well as fight effectively does come in handy when you are confronted with a single guard, for example.

As you use stealth in the game you can also unlock perks that make you harder to see, more quiet, more proficient at hacking, or that allow you to use skills more often. These perks unlock automatically and stack with abilities and stats that come from leveling your character and outfitting him with various equipment.

Which brings up yet another way to ensure Agent Thorton will be stealthy: Equipment. Firearms can be equipped with silencers and other technology to make them more quiet, and as mentioned already, pistols can use tranquilizer ammo. Armor can be made more stealthy, and there are several gadgets that make it much easier to get through the game without enemies swarming all over you.

As far as the actual quests in Alpha Protocol, they don't all lend themselves well to stealth but most do. Some missions will explicitly expect you to use force but you can still use tranquilizer ammo to sedate enemies, for example. But it's probably unrealistic to expect to make it all the way through the game without killing a few enemies.

If you do choose to use stealth instead of always going in guns ablazing, expect to reload checkpoints frequently so you can try various tactics until you get it right. You will find that in general, you can make it through large portions of the game without ever killing a single person.