Shinobi Organisational System

Although there are variations from village to village, the general organisational structure and hierarchy of the ninja systems of each village is about the same. At the top of the organisation is the village head, or the Kage in the case of the Five Great Shinobi Countries. They rule the village and its shinobi together with a council, usually consisting of highly ranked shinobi and elders.

The actual shinobi forces are divided in three groups. The regular forces, the Anbu, and the medical teams.

Regular Forces
The form the foundation of the village and its shinobi system. The majority of shinobi are a part of these forces and together, either individually or in teams, they perform the majority of the missions the village receives. They are also tasked with the various duties within the organisation, such as training and administrative duties.

When an Academy student graduates, they usually become a part of these forces, assuming the rank of genin. Via various exams and tests, they can be promoted to higher ranks, first to chūnin and jōnin after that. Sometimes, when a shinobi is specialised in a very specific skill, they can assume the rank of tokubetsu jōnin, which is a rank between chūnin and jōnin.

Ranks
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Teams
Although the higher-ranking members of the regular forces often perform missions alone, most are done in teams. The most basic team is the one a genin is placed in after graduation. This so-called three-man cell consists of three genin under the guidance of a jōnin commander. These teams are meant to give the new shinobi practical skills, while already being a productive member of the organisation. Usually, strong bonds are cultivated between the members of such a team, lasting their entire lives. Because of these bonds and the fact that working with one's long-time team-mates is usually more efficient, these teams often last even after all members have been promoted to chūnin or higher.

Besides these basic teams, there are also teams, and groups created for specific missions and tasks. Sometimes these are ad hoc teams which only exist for the duration of the mission, such as the Sasuke Retrieval Team, but in certain cases these teams are more organised and lasting, such as the Nijū Shōtai, created to battle the threat of Akatsuki.

Special Ranks and Functions
Besides the standard ranks of genin, chūnin, tokubetsu jōnin, and jōnin, there are some shinobi who bear a special rank or function. For instance, Kumogakure has a rank between that of jōnin and Raikage which is known as "Head Ninja". This person helps in leading the shinobi forces and is capable of representing the village officially. Konohagakure has the Jōnin Commander, who is selected from the jōnin population to represent the regular forces in council meetings and likely helps in commanding the regular forces.

Groups
There are various groups within the Anbu, aimed at various different functions and tasks. Kirigakure, for instance, has the hunter-nin — a group created solely for hunting down and disposing of missing-nin. Konohagakure has the ANBU Torture and Interrogation Force, who interrogate prisoners and work to gather intelligence. Though they were to officially disband, another Anbu faction named Root carried out extremely secretive missions and were not under the direct authority of previous Hokage.

Medical Teams
The is the supporting side of the shinobi forces. They consist of medical-nin, working behind the scenes to heal sick and injured shinobi and to make sure the organisation's resources are always in peak condition. Medical-nin are similar to a Hospital Corpsman or HM of the military in real life. They also do extensive research into new techniques, medicines, diseases and the human body. Although not seen very often, they are highly respected. Even to a jōnin, the advanced skills of these shinobi seem like magic.

Not all medical-nin are members of the medical teams, though. There are also medical-nin within the regular forces, who go along on standard missions to increase the success-rate referred to as field medical-nin. Though medical-nin from the hospital are sent out into the fields from time to time as seen when a group of medical-nin were sent after the Sasuke Retrieval Team. However, back in the village, it is the medical teams who run the hospital and treat the wounded.