Skills are classed in two types, General Abilities and Investigative Abilities.
Investigate Abilities can be stuff like Flirt, Cryptographcy, Notice, Forensic Accounting, Architecture. You typically have 0-3 ranks in them (0 means you don't have the skill.)
As a GM, you design your story to contain certain "core clues". When the players analyze/investigate a situation (be it a crime scene, a rock formation or whatever), and they have the right skill, you give them a core clue automatically. Basically the only thing to figure out a core clue is
- Be at the right place
- Describe how/that you are using a skill
There is no skill roll or check, the success is a given. These core clues should be sufficient to advance the investigation and give the players hints where to go next.
You can also include additional clues, that give extra benefits. These require a "spend". You can make as many spend sin a skill as you have ranks in it, and they refresh generally after the mission/adventure is concluded. Players can also suggest possible spends for a skill for additional benefits.
Generally, the focus is more on how do you approach the investigation (whether you bully someone in revealing information or flirting with them for example) and how you interpret the clues you find.
Example:
1) Flirting
So, your flirting with the secretary might reveal that her boss is currently at his psychatrist and will not be back in the office before tomorrow. A spend might allow you to distract her enough to catch a look at his schedule and figure out the name of the psychatrist and her bosses other appointments today. (Or maybe a player suggests spending a point to get her phone number to build a relationship and turn her into an asset, which might be a Night's Black Agents thing.)
2) Forensic Accounting
Forensic Accounting might allow you to figure out that a business acts just as a front for a big money laundry action and where the money is generally coming from. A spend might reveal to you the point of highest vulnerability (say, a major figure that if exposed would bring it all down, or the place where all the money is accounted for and distributed.)
The General Abilities are in some ways more like traditional skills - you roll the dice to see if you succeed. The difference is that the skill rank alone doesn't do anything. You have to actively spend points to raise a skill roll. This is obviously a very unusual mechanic and I know that it's a bit challenging for players to get into this. (At least that's the case for my players).
So, you might have Shooting 12 (which is pretty good). If you want to shoot someone, you roll 1d6. The DC is typically 3 or 4 in this case and will be higher for special enemies. If you want to increase eyour chances of hitting, you can spend points of your skill. Again, you only add something to the roll if you actually spend points from the skill. If you hit, you roll something like 1d6+/-x (depending on the weapon chosen) and the target substracts the damage from its health. (Health is, by the way also a general ability.)
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I don't know how many of these things are unique to Night's Black Agents, but some skills have specific benefits associated with their ranks. For example, if you take Drive, for each rank, you can choose one type of vehicle that you can drive.
Contacts is a skill that allows you to describe contacts your character can use to get information or aid. Covers are cover identities that gives the player the chance to access information or acquire help that's only available to someone in that cover. (Say, if your cover is that of a Smithonian Art Procurer or whatever.)
The unique thing about these skills is that you can choose to leave the details blank and only fill them in as the need arises. So, when you need to talk with a mafia boss, you can decide that you once operated under the cover of a respected mafia enforcer and use this to contact him. Or if your team finds an V-22 Osprey, you can decide that you actually know how to fly it. So to some extent, your character is actually fleshed out in play.
The extra-unique thing about Contacts and Covers is that they can be burned - the points with them don't refresh. SO i fyou used a contact one too many times, he'll be no longer available to you (maybe he's tired of all the favors you ask, or the opposition takes him out, or he gets fired from his job for helping you one too many times). If you use a cover one too many times, it is blown. ("Funny, whenever Leone the Mafia Enforcer crops out, something bad happens to our people there. General Advice: Shoot on Sight").