The ninja form a functional counterculture to the samurai. To normal society they are outcasts. Those discovered to be ninja are shunned. Ninja caught performing acts of terror or espionage are subject to immediate and shameful execution. Despite this, ninja are often found serving samurai lords for whom they accomplish deeds that those warriors feel unable to attempt within the bounds of their honor. Ninja become spies, reconnaisance teams, terrorists, security specialists, and assassins for samurai lords.
Ninja, for their part, consider themselves to be apart from the culture of the ruling castes of Nippon. Their goals and methods differ although some of their attitudes are the same. They do not consider themselves specifically bound by the code of bushido although they adhere to ninja versions of loyalty, honor, and courage.
Ninja are organized into "clans" or "traditions" which share martial techniques and social philosophies. Such clans mimic samurai clans in their structure and web of obligations. Some are high-minded and develop their arts for their own protection, to aid the oppressed, and to maintain the proper balance of powers in the world. Others, having divorced themselves from society, see themselves as free from its sanctions and restrictions, and operate on an amoral, mercenary basis.
Whatever their motivations, ninja are secretive. They spend most of their lives in seclusion, in a cover identity as a normal member of society, or in a bewildering succession of disguises. They keep their skills within their clan. It is rare that an outsider is taught any of their secrets. Like typical Nipponese, they are intensely loyal to their clans. Breaking the veil of secrecy is considered a betrayal of the clan, leaving the betrayer clanless and subject to death.
Obviously, a code calling for truth is incompatible with the secret operations of ninja. They are, however, scrupulously honest in the matter of contracts. Failure to properly execute a contract requires the death of the agent(s) responsible. Such responsibility is not passed on within the clan in the fashion of a samurai clan or family. Only the ones who are at actual fault will suffer, even if the clan itself must punish the guilty survivors.
The ninja is unhampered by the inflexible honor code of the samurai. Failure of one ploy can be remedied by the success of another. Unlike samurai, ninja are not disgraced by capture, if an escape can be arranged. Still, capture usually demands death - to avoid revealing secrets. A death which leaves the body unidentifiable is preferable, since recognition of a ninja could lead to the exposure of others who operated with him.
Ninja are pragmatic. They will use any and all means to accomplish their ends. Ninja avoid fighting and, if forced to fight, will try to win by any means, fair or foul. They have even been known to simply run away from an opponent, a dishonorable action for a samurai.
To guide you, here is an outline developed from the historical Togakure-ryu of Iga province. The clan tends toward isolation, but will undertake justifiable missions, combat and espionage contracts preferred. Skills emphasized include Disguise, Martial Arts, and Throwing. Favored weapons are ninjato, bo staff, shuriken, spears, bisento (a characteristic weapon, similar to the naginata), and kusari-gama. Characteristic devices include explosives, a four-pointed shuriken, tetsubishi, shinobi-zue, and nekode.
The clan master is called the jonin. He makes policy, approves contracts, and devises training regimens. His actual identity is usually concealed. sometimes a jonin may even hide his identity from his clan, leaving and receiving identifiable messages in a dead-drop to be acted on by his subordinates. Some historical jonin maintained two or more complete families in different locations as cover identities.
Beneath the jonin are the chunin, the middlemen. They are the clan elders, retired or incapacitated field agents, skill specialists, and teachers. Chunin oversee training of agents and administer the day-to-day activities of the clan. When someone wishes to hire a ninja, he must negotiate with a chunin. Of course, the chunin will rarely admit to being ninja. He will instead speak of knowing "someone who can help." Chunin rarely undertake missions themselves.
The field agent and common clan member is called a genin. genin are the "soldiers" of the clan.
Some common skills and abilities the ninja have differ somewhat from what is common.
Disguise: Ninja have some special advantages when using this skill. Besides disguising themselves as specific persons, ninja are especially skilled in five more general disguises. These disguises are called the "five ways of going." They are: a travelling entertainer (some entertainment skill or skill usable as entertainment helps), who can travel freely across the land; a wandering Buddhist priest or yamabushi, welcome almost anywhere in Nippon; a simple peasant, often ignored by samurai; a merchant, free to travel and expected to inquire into current events; and a "blind" masseur, also free to travel and someone in front of whom customers talk freely.
Hide: Ninja are extraordinarily proficient at hiding. They are even able to sometimes hide where no other would find any cover, like an open field, an empty room, a leaf-bare tree and so on. Ninja may hide where a casual viewer would never think to look, like among the rafters of an empty room.
Ninja also have a sign language they may use to convey silent messages to confederates.
Yogen: Yogen is the knowledge of the mysterious compounds, dusts, poisons, and potions used by ninja.
Variants on the garb come in other colors for concealment in special circumstances such as white for snow, dark green for heavily vegetated regions, and brown for areas of bare earth. Under the proper circumstances, the color aids in concealment. Sometimes the clothing is reversible, with the standard black on one side and normally colored clothing (for a quick disguise) or a second camouflage color on the other.
Some explode on contact and some use fuses. Fuses must be lit by a source of fire such as flint and steel, a doka, or a candle, but are notoriously unreliable and may go out.
Bombs are large and hard to conceal. They are used in defense of clan holdings and special sabotage missions. They use fuses and may not be thrown. A typical bomb is quite powerful, but is a rather primitive affair.
Flashbombs are small and easy to conceal. They explode on impact, causing a bright flash that will blind anyone looking at it for a short period of time unless that character happened to look another way or close his or her eyes in time. Creatures with eyes adapted to night vision is more adversely affected.
Grenades are small, concealable versions of bombs. They have a small blast radius, usually about 2 meters.
Incendiaries come as grenades or bombs. They give off a flash like flashbombs when they explode but do not cause any damage as such. Instead they have a chance to ignite any flammable material within their area of effect. A fire in the lightly-built and easily-inflamed structures of Nippon may be devastating, and as such these bombs are often used in sabotage.
Powders for internal use must be slipped into the target's food or forced down his throat. Powders for external use may be loaded into "eggs" or used in a metsubishi. A metsubishi is a small box-like device with a mouthpiece on one end and a hole on the other. The ninja places the powder into the box, places his lips to the mouthpiece, and blows into it to expel the powder out the hole.
Blinding Powder (external, immediate): Temporarily incapacitates the victim unless he avoids getting it in his eyes and nose.
Blood Powder (external, immediate): Designed to coat a victim and make him attractive to carnivorous animals. A ninja may then release such animals to attack the victim.
Poison (internal, time variable): Comes in a great variety of types.
Stink Powder (external, immediate): Used like blood powder to coat a victim. The stench which clings to him is used as an aid in tracking or a ruse to get him to remove stinking armor or clothing.
Concealed sword and dagger blades are the simplest and their use is obvious. A hollowed staff may conceal a weighted chain to be shaken out in the same motion it takes to attack with it. Spring-loaded blades may be set to jump out to fighting position or to fire from the shinobi-zue like a shuriken. Range for such weapons is poor, about 5 meters.
Some shinobi-zue are set to release a dose of powder with a flick of the wrist, even though the range is only 3 meters.
This serves a dual function: any enemy touched will not know the ninja's true location, and the ninja's sword remains ready for action.
A scabbard may be rigged to expel a dose of powder when an iaijutsu draw is performed (the target of the powder and the sword attack will be the same).
The scabbard, with end cap removed, may be used as a blowgun to propel darts. Darts are most useful for introducing an internally-effective compound into a victim.
A dozen tetsubishi may be scattered carefully over a square meter, giving a good chance that a person passing will step on one.
Air Bags are used by ninja for hiding underwater or swimming below the surface for fairly long distances. A makeshift air bag will only hold a gulp of air, while good ones may hold up to four times that amount of air.
Floats are also used but do not keep a ninja's devices dry. A ninja need not exert himself unduly and need not worry about drowning unless he loses his float. A ninja may construct a float from an animal skin or a collection of hollow gurds.
Water Shoes are large, basket-like devices worn over the feet and lower legs. The ninja balances upright and propels himself with a paddle. He thus "walks on water." Water feet may only be used on calm water such as a castle moat or slow-moving river. This method allows the ninja to cross water without immersing any powders or explosive weapons he is carrying. Of course, in the event that he capsizes, he will be hindered by the device until he either drowns (in which case the question is moot), or can get rid of the water shoes.