Skills list a variety of things useful to shinobi, though rather than special techniques (such as jutsu) or unique styles of combat (like Abilities), these are what could be considered job-related talents; an accountant needs to be able to balance the books, and a ninja needs to be able to sneak.
Skill checks are rolls on 1d20, plus the relevant stat (listed in parenthesis next to the skill name) divided by 10, plus the skill's rank. For example, if you had 86 Dexterity and 4 ranks in the Stealth skill your Stealth roll would be: 1d20+8+4
If you have no ranks in a skill you instead take a -2 penalty to that skill roll. You may not benefit from more ranks in a particular skill then the relevant attribute modified. So in the above example you could not benefit from more then 8 ranks in the skill. That is, you can never receive a bonus from skill ranks to your d20 then you receive from your relevant attribute.
If a skill says "Trained" next to it, that means you cannot make a skill check for it unless you actually have ranks in the skill. These generally represent things that actually require a degree of knowledge to do at all. Anyone can look around or try to hide behind a tree, but things like proper knowledge of how to prepare poisons and keep them virulent, or how to identify those poisons and the appropriate treatments just by their symptoms, are not intuitive.
Skills cost 5 CP to purchase the first rank. All ranks after that cost the Current Rank+1 CP. Skills also take two weeks to train to improve, three weeks for the first rank. See character Advancement for more details.
Athletics (Varies) Edit
You use the Athletics skill whenever you perform any acrobatics, attempt to run fast or for a long time, lift something heavy, climb, and do anything else physical. STR is the attribute that modifies this when you do things such as try to lift something heavy, jump, or climb. AGI is checked when you need to know how fast you do something, like running or swimming. DEX is for when things need to be precisely or with finesse, for instance diving. END would be checked if you need to perform a physical activity for a long period of time, such as running a marathon.
Awareness (MND) Edit
How good you are at noticing things. This covers a broad range of situations, from spotting details that are out of place to trying to find a specific body on a battlefield, to managing to pick up what only a few people are saying in a crowded room.
Espionage (MND) Edit
This applies to almost any situation where you need to do something sneaky and ninja-like, beyond just walking around without being seen. Sabotaging defenses, setting traps to not go off without making it look like they've been tampered with (this may at times require a combined larceny check), figuring out which documents to take from a pile (and making it look like you hadn't been searching through it), knowing common ways to protect against and detect intruders, and things such as that are all important. You are sensitive to body language, speech habits, and mannerisms of others.
Knowledge (MND; Trained) Edit
Knowledge actually encompasses a number of unrelated skills. Knowledge represents a study of some body of lore, possibly an academic or even scientific discipline. Example fields of study are; Jutsu Theory, Clan Knowledge, Village Knowledge, Current Events, Architecture, Nobility, Nature, Geography, etc.
Larceny (DEX) Edit
This skill is relevant to picking locks, solving combinations and puzzle locks. It applies to acts of manual dexterity such as lifting an item from a target and hiding it on yourself, palming an unattended object, or anything from disarming a trap, jamming a lock, or rigging a carriage wheel to fall off.
Medicine (MND; Trained) Edit
Your knowledge of the human body, how it works, medical treatments, and related topics. This ranges from how to effectively stop bleeding without making the person in question lose their limb to details about anatomy. You may not take this skill unless you have Research at 10 or more.
Poison (MND; Trained) Edit
This is how good you are at using and identifying poisons. Although it's main use is actually using those poisons, it's also helpful to have if you need to treat them.
Research (MND) Edit
This is more than knowing how to find important, specific bits of information in a sea of unrelated details (such as a book). In addition to trying to secure tidbits of information, it can help you make sense of complicated codes or ciphers, know who to talk to to keep up to date on rumors, and anything like that.
Stealth (DEX) Edit
Your ability to sneak, keep yourself out of view, and not be obnoxiously loud. This is used to simply keep your position unknown, as well as actually moving from point A to point B without being noticed. A ninja who isn't adept in this isn't likely to get very far in their career unless they have some very significant redeeming qualities.
Survival (MND) Edit
This skill lets you forage for food and move easily through a hostile environment, or in less then optimal conditions. It also helps to prevent you from getting lost. Finally, it represents your ability to track others and resist being tracked yourself. You must score at least a 20 to successfully track someone through any environment. If the person you are trying to track is actively avoiding you, then they may make an opposed survival check. You take a -1 penalty to track someone for every day old the trail is, or for every hour the trail is old if the environment works against you (rain, snow, etc). Visibility penalties also apply.