There are several types of skills in the game. The main two kinds are red and blue skills. Red skills increase your own abilities and powers, while blue skills are more about detection and can be shared via the SOP system. Both types of skills can be leveled up with use. You have four slots for skills in total.

Red skills are divided into weapon bonuses and miscellaneous bonuses. Weapon bonuses increase your skill with a certain weapon type, and are leveled up by using that weapon. Handguns, SMGs, shotguns, assault rifles, sniper rifles, traps, CQC, knives, and grenades fall into this category. Firearm skills (all the guns) help with recoil and accuracy; the "trickster" skill increases the speed you lay traps; the "quarterback" skill increases throwing distance for grenades; possessing the CQC skill allows you to get enemies in chokeholds, and increasing the level increases the damage you do with it (for faster knockouts). The knife skill allows you to move around while wielding a knife, and having it at level 3 allows you to slit throats with it (only when paired with CQC level 1). Higher level weapon skill generally take more slots to fill up, with firearm skills taking up the most. Miscellaneous bonuses include runner (increases speed), hawkeye (increases zoom rate when using first person mode), and surveyor (increases max lock-on distance). Runner is all right, but the other two are pretty much useless and overly specific.

Blue skills all affect detection, and the things you detect are shared through SOP. Blue skills level up by fulfilling whatever job they have, and leveling them up makes them display either for a longer period of time or with a larger range. Monomania highlights any enemy you shoot (higher level = longer period of illumination) allowing your allies to spot and target them. It is especially useful when paired with grenades, as you can see where enemy bodies have been thrown and attack while they are down. Sixth sense detects traps (mines and magazines), and is useful if you yourself are using traps (they aren't otherwise marked on the map, and your allies may easily stumble into them). Narc is a weird one; if you are locked onto an enemy and that enemy damages you, he will be highlighted. Scanner is perhaps the most unique skill, and it must be paired with at least one level of CQC. When you have someone in a chokehold, having scanner allows you to select the scanning plug item and inject them with it. When you do so, all the SOP data they are connected to will become available, and all their linked allies will be highlighted on your display and the display of the people you are connected to. Higher level increases the length of time they are highlighted.

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