The ninja are a development of continual Japanese wars after 1330 AD. They almost certainly didn't exist before that time.
The ninja are a counterculture to the samurai. They are considered outcasts in normal Japanese society. Those discovered to be ninja are shunned. Ninja caught performing acts of terror or espionage are subject to immediate and shameful execution. Despite this risk, ninja are often found serving samurai lords for whom they accomplish deeds that samurai feel unable to attempt within the bounds of their honor. Ninja serve as spies, reconnaissance teams, terrorists, security specialists, and assassins for samurai lords.
Ninja consider themselves to be apart from the culture of the ruling classes of Japan. Their goals and methods differ although some of their attitudes are the same. While they are not bound by the code of Bushido although, they adhere to ninja codes of loyalty, honor, and courage.
Ninja are organized into clans or traditions which share fighting techniques and social philosophies. Ninja mimic the structure of samurai clans in their network of obligations. Some traditions develop their arts strictly for their own protection, to aid the oppressed, and maintaining the balance of powers in the world. Others have separated themselves from society and consider themselves free from its restrictions, operating on a mercenary basis.
Regardless of their motives, ninja are always secretive. Most of their lives are spent in seclusion, in a cover identity as a typical citizen of society, or in an intricate succession of disguises. They keep their skills within their clans. It is an extreme rarity that an outsider is taught any of their secrets. Like most Japanese, ninja are intensely loyal to their clans. Breaking the veil of secrecy is considered to be a betrayal of the clan. Betrayers are subject to a typically slow and painful death.
Obviously, a code of truth would be incompatible with the secret operations of ninja. They are, scrupulously honest in matters of contracts. Failing to properly carry out a contract requires the death of the agent(s) responsible for its completion. This failure is not passed on to the rest of the clan as with samurai clans. Only the individual ninja are at fault and suffer.
The ninja is not encumbered by the inflexible codes of honor that bind samurai. Failure of one ploy can be redeemed by the success of another. Unlike samurai, capture is not dishonorable to ninja, so long as an escape can be made. Capture usually means death for a ninja - as to avoid revealing secrets. Ninja prefer a death which leads the body unidentifiable. This is needed because recognition of a ninja could expose others who have worked with him.
Ninja are pragmatic in their actions. They use any and all methods at their disposal to accomplish a mission. Ninja prefer to avoid direct combat. When forced to fight, they use any means (fair or foul) to ensure their victory. Ninja have even been known to simply flee from an opponent, an action which would be considered dishonorable for a samurai.
As mentioned above, ninja "traditions" are modeled after samurai clans. Each "tradition" is devoted to a specific philosophy such as mercenary sale of abilities, non-interference with society in general, and others. In most instances, the clan will have one or more skills or devices it favors. These skills and/or devices usually go along with their preferred contract type.
The following outline was developed from the Togakure-ryu of the Iga province of Japan. The clan tends towards isolation. However they will take missions they deem justified. Espionage and combat contracts are preferred. Disguise, Martial Arts, and Throwing are skills emphasized by the Togakure-ryu. Their preferred weapons are the bo, spears, shuriken, kusari-gama, bisento (a weapon similar to the naginata), and the ninjato. Their preferred devices include nekode, tetsubishi, explosives, shinobi-zue, and a four-pointed shuriken.
The clan master is called the jonin. The jonin approves the clan's contracts, develops training regiments, and makes clan policies. His identity is usually kept secret, sometimes even from his own clan. These super-secret jonin use a dead-drop to leave and receive identifiable messages for his subordinates to act on. Some jonin have maintained two or more separate families in different locals to use as cover identities.
Below the jonin are the chunin, the middlemen. Chunin are the elders of the clan, either retired or incapacitated field agents, teachers, or skill specialists. They administrate the daily activities of the clan and oversee training. When a person wishes to hire a ninja, he must negotiate with a chunin. The chunin will almost never admit to being a ninja himself. Instead, he will speak of "knowing someone who might be able to help". Chunin rarely undertake field missions themselves.
The common member of the ninja clan is called a genin. They are the field agents and the "soldiers" of the clan. It is the genin who actually carry out most of the clan's contracts.
Ninja receive training from childhood by their families. General athletic skill, suppleness, and toughness are emphasized early in life. Specialized ninja skills and fighting are added to the training regiment later in life.
There are a few skills that are common to almost all ninja clans. Here are two of the most common.
Disguise: Ninja need to be adept at keeping their status as ninja secret, so they have learned how to disguise themselves. Ninja can disguise themselves as a specific person. However, there are five more general disguises that the ninja uses. These disguises are know as "the five ways of going." They are:
Hide: Ninja are incredibly adept at hiding. They are known for being able to hide where another person would find no cover, such as an open field or an empty room. Ninja may hide where the casual viewer would never think to look, like among the rafters of an empty room.
ninja also use a type of sign language to communicate silently with fellow ninja.
Nawanukejutsu: This skill allows a ninja to escape from bonds. This process is easily visible to any onlooker, and can be interfered with. A ninja may use this skill to slip through openings that are normally to small for a person of the ninja's size. Ninja develop the suppleness required for this skill through childhood training.
Yogen: This is the mysterious knowledge of mysterious compounds, potions, dusts, and poisons used by ninja.
Ninja armor is made up of a hood and shirt of fine chain mail, (which is uncommon in Japan). This mail; which protects the ninja's head, arms, and torso; is worn under the clothing. Mail pants are often added to the outfit for major battles and assaults on strongholds.
The ninja climbing pole is a 3-meter long pole with collapsible rungs. A hook can be fitted to one end of the pole for a more secure hold. It breaks down, through sections which slide into each other, into a 1-meter length. This makes the pole easier to transport and conceal. It is used as a ladder and a probe.
The ninja garb comes in other colors for concealment in special circumstances; white for snow, dark green for heavily vegetated areas, etc. Under proper conditions, the color aids the ninja in concealment. The clothing is sometimes reversible, with the standard black on one side and normal colored clothing or a second camouflage color on the other.
A doka is a small container used to safely carry live coal. The device is useful for warming the fingers for a delicate task or lighting a fuse with little fuss.
"Eggs" are small containers used to deliver various powders to a target in combat. They shatter on impact, releasing the powders in a cloud.
Ninja use various devices employing gunpowder and other explosive chemicals, well kept secrets among the clans. There are four categories that cover explosive ninja weapons: bombs, flashbombs, grenades, and incendiaries.
Bombs are large and difficult to conceal. They are typically used to defend the clan's and special sabotage missions. They use fuses and may not be thrown. Typical bombs are quite powerful but primitive.
Flashbombs are small and easily concealed. They explode on impact, creating a bright flash of light that will temporarily blind anyone looking at it unless they protect their eyes in time. Animals with eyes adapted for night vision are more adversely affected by flashbombs.
Grenades are small, concealable versions of ninja bombs. The are less powerful than bombs and have a smaller area of affect, usually about a 2 meter blast radius.
Incendiaries can be grenades or bombs. These give of a flash like flashbombs when they explode but their main affect is to ignite all flammable material in their area of affect. These bombs are often used in sabotage missions.
The kawanaga is a grappling hook with one to three prongs attached to a rope. Besides its obvious use, ninja learn to use the kawanaga as a weapon. Although, as with all multi-purpose ninja devices, it is not as effective as a dedicated weapon.
The Kyotetsu-Shoge is a ninja "chain weapon". It is very similar to the Manriki-Gusari in design. It consists of a dagger, with a curved projection on one edge, at the end of a 3-meter long rope. A metal ring, about 6 inches in diameter, is attached to the other end of the rope. Aside from its use as a weapon, the Kyotetsu-Shoge doubles as a makeshift grappling hook.
Nekode , also known as shuko, are the ninja version of the fighting claw. The claws fit in the palm of the hand on a metal band. The band allows the ninja to parry blades with nekode. The metal claws allow him to trap a blade and either disarm his opponent or break his sword. Nekode and ashiko, a similar device for the feet, can be used to aid a ninja in climbing
Ninja have developed several powders of use to them. Some are applied externally while others must be take internally to have any affect. Some powders have immediate and temporary affect while others need time to work but have more permanent affects. Powders are measured in "doses" which are determine by the amount needed for the desired effect and/or to fill a delivery container. Powders requiring internal use must be secreted into the victims food, or forced down his throat. Externally acting powders may be loaded in "eggs" or used in a metsubishi. A metsubishi is a small box-like device with a mouthpiece at one end and a hole in the other (similar to a blowgun). The ninja places the powder in the bow, places his lips to the mouthpiece, and blows to expel the powder from the hole.
Here are a few examples of powders used by ninja.
Blinding Powder(external, immediate): Temporarily blinds the target unless they avoid getting it in their eyes and nose.
Blood Powder(external, immediate): Designed to coat the target making them more attractive to carnivorous animals. Ninja often release such animals after marking a target with blood powder.
Poison(internal or external, variable time): comes in a variety of types and affects.
Stink Powder(external, immediate): similar to blood powder. It is used to coat the target making them easier to track or as a trick to get them to remove smelling armor or clothing.
Shinobi-Zue refers to various devices consisting of a weapon concealed in a stick or staff. these hidden weapons will pass casual inspection outside of handling them. Even then only their unusual weight is obvious.
The scabbard of the ninjato has a variety of uses. The sageyo cord may be removed and used as a garrote. It may be rigged to expel a dose of powder when an iaijutsu draw is performed. The end cap may be removed converting the scabbard into a makeshift snorkel. Also with end cap removed, the scabbard can be used as a blowgun to introduce internally active compounds to a victim.
Tetsubishi, also known as mitsubishi or makibishi, are small pyramidal devices designed to always present at least one point upwards. Bare feet or thin soled footwear of a running person are easily pierced by the points, severely diminishing their mobility. Ninja often coat tetsubishi with poisons to further injure anyone stepping on them. Tetsubishi are often used in conjunction with ball bearings and spurjacks. A person will slip on the bearings and spurjacks and fall on the tetsubishi.
Here are a few water crossing devices used by the ninja.
Air Bags are used to hide underwater or swimming below the surface of a body of water for fairly long distances.
Floats are used to keep a ninja's devices dry. The ninja need not exert himself unduly or be concerned with drowning, unless he looses his float.
Water Shoes are large basket-like devices that fit over the ninja's feet and lower legs. The ninja balances upright and propels himself with a paddle. He thus appears to "walk" on water. Water shoes can only be used in calm water like castle moats or slow moving rivers. The use of water shoes allows the ninja to keep his powders and explosives dry while crossing bodies of water. If the ninja capsizes, the device severely hinders him until he either drowns or can remove the water shoes.
Ninja tend to disregard magic in favor of technology and finely honed skills. Since many ninja live close to the land spirit magic is usually preferred because it is easier to interact with the kami. However, some ninja do practice true sorcery. A few clans specialize in the use of magic over devices. These clans favor spells which duplicate the effects of devices.