Skills represent broad, generic things ninja do, and how well your character can do them. Unlike abilities or jutsu, the exact method of performing a skill is ambiguous; you might use stealth by hiding in foliage, or by camouflaging yourself, but in game terms it’s all about the same.
Your skills all have a limit of 5 +(your total XP)/200 ranks. A lot of them benefit from practical application and general worldliness. Actually increasing your skills up to that limit, however, requires you to spend skill points.
You start with 10 Skill Points, and get 1 Skill Point for every 25 XP you gain; this happens automatically, for free, and you cannot buy more skill points. Clanless characters gain 1 skill point for every 20 XP instead.
A single skill point raises a single skill by one rank.
For example, if you had 600 XP you would have a total of (10 + 600 /25 =) 34 skill points, and you could raise any of your skills up to rank (5 + 600/200 = ) 8. You could use this to raise your Stealth to rank 8, your Awareness to 8, Chakra Control to 8, Resistance to 5, and Survival to 5 (8 + 8 + 8 + 5 + 5 = 34). A skill roll is 1d20 + (your ranks in the skill). Even if you haven’t raised a skill beyond zero, you may still make a plain 1d20 roll when attempting to perform a task that would call for that skill.
Some skills are labeled “Trained”, which means you cannot make any roll at all unless you have at least 1 rank in them. These are generally skills which represent knowledge you have to learn, instead of something that can be attempted intuitively.
You use athletics when you perform acrobatics, leap across a chasm, try to navigate difficult terrain, weave your way between traps, swim across a river, or so forth. You can flip, tumble, and keep your balance under difficult circumstances.
How perceptive you are. This applies to things like hearing a faint noise, noticing that you’re being followed, spying on a single conversation in a crowded room, and finding an enemy hiding from you in combat.
This is your ability to control the flow of the chakra within your own body, using it efficiently and shaping it precisely to do what you want. To a limited extent, it also represents how intuitively aware you are of the nature of chakra in general, and might allow you to notice when something’s unusual about the surrounding chakra.
Something of a catch-all skill, this includes most things shady and underhanded. Pickpocketing, lock-picking, setting and disarming (or sabotaging) traps, forging documents, sleight of hand, and disguising yourself all fall under the umbrella of espionage.
You have knowledge of the human body and how it works. This includes biology, first aid, and at higher levels actual medical procedures and requirements. With a few ranks, you can probably apply a tourniquet; with enough, you might even deserve a ‘Doctor’ in front of your name (but good luck actually getting any respect!).
Book smarts, overall knowledge, and an ability to gather information. Research can be used to solve complicated code and ciphers, find information in a library, and get up to date on the latest gossip when in a new town.
Not to be confused with resilience, this is how well your body is able to fend off the ravages of the environment and all sorts of unpleasantness that might befall it, from blistering heat to poison to burns. This is primarily useful for fighting off unpleasant status effects that may afflict you, both in combat and out.
How well you can sneak around, keep out of view, and not be obnoxiously loud. Whenever you need to be unobtrusive, hide from enemies, or move from point A to point B being noticed, stealth is your best friend. A ninja who can’t be stealthy probably won’t get very far in their career without some significant redeeming qualities.
This lets you forage for food and move easily through hostile environments. While resistance might keep sunburn at bay while stranded in the desert, survival will help you find the nearest oasis and make an umbrella out of palm fronds. It’s also used to track people and animals, and avoid being tracked.
This represents overall familiarity with poisons. While high enough medicine might be able to identify a poison, its symptoms, and how to treat it, toxicology knows what plant or animal that poison comes from, how long it takes for effects to set in, and just how deadly it can be. Many medics have enough of this skill to be helpful in their work… but it’s also very handy if you find yourself needing to poison someone.