Shinobi Organizational System
Although there are variations from village to village, the general organizational structure and hierarchy of the ninja systems of each village is about the same. At the top of the organization is the village head, or the Kage in the case of the five major villages. 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.
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Regular Forces
The regular forces (正規部隊, Seiki Butai) 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 organization, such as training and office work.
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 after that to Jōnin. Sometimes, when a shinobi is specialized in a very specific skill, they can assume the rank of Tokubetsu Jōnin, which is ranked between chūnin and jōnin.
Ranks
Academy students
Academy students (忍者学校性, Akademī-sei) make up the student body of the Ninja Academy, where they are trained and prepared for life as a shinobi. They are not an actual part of the shinobi force, as they are still in the process of mastering the very basics of the ninja lifestyle. However, they can be conscripted as part of the war potential in times of emergency.
Academy students spend their time honing the various skills they are required to have and undergoing various tests and exams to see how they progress. Besides ordinary school subjects such as history and mathematics, they are taught the basics of Ninjutsu, Taijutsu, and most likely also Genjutsu. This includes learning about chakra and how to control it, tactics, hand seals, and several E-rank techniques, such as the Clone Technique and the Transformation Technique. They are also trained in working both individually and in teams.
Eventually they are given a graduation test to see if they are ready to try and become Genin. Passing this test does not mean automatically grant them this title, as they need to pass a second test given by their Jōnin instructor, but they do receive a forehead protector. Those who fail either of these tests are sent back to the Academy. The requirements for graduating vary from village to village. In Konohagakure, the Academy students simply have to show their proficiency in a randomly selected E-rank technique. In Kirigakure, however, the test was a life-or-death battle at one time. A practice since changed, after Zabuza Momochi massacred an entire graduation class.
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Genin
Genin (下忍, Genin; Literally meaning "Low Ninja", Meaning (Viz) "Junior Ninja") are the lowest level of ninja and also the ones that display the most difference in power. When they become Genin, ninja start to do their bit for their village's economy – being sent on missions that the village gets paid for. They are typically sent either on D-Rank missions, which are almost entirely risk-free jobs of manual labor, or, very rarely, on C-Rank missions, which are a cut above that and begin to verge on real "ninja" work that have a very low possibility of risk to the ninja involved. When Konohagakure was shorthanded in upper-level ninja because of the attack by Otogakure and Sunagakure, the village had to occasionally send Genin on higher-ranked missions.
Genin are put in four-man cells or squad, consisting of three Genin and a Jōnin-sensei, in order to learn teamwork and experience true ninja life under the supervision and protection of an elite shinobi. The make-up of these teams is based on the individual skills of the Genin, so that there will be a balance between the teams. For instance, Naruto Uzumaki, who passed with the lowest grades, was put in a team with Sasuke Uchiha and Sakura Haruno, who passed with the highest grades and highest written exam scores, respectively. The teams are usually made up of two boys and one girl, though there are exceptions.
Due to the fact that Genin are the lowest level ninja, they normally provide limited use during dangerous missions (B-rank or higher), and are usually only capable of successfully completing E or D-rank techniques. However, it should be noted that Genin is simply a rank, and is not always an accurate representation of a ninja's skill level. Naruto Uzumaki is still a Genin, but regularly goes up against the S-Class criminals of Akatsuki.
Though Genin are relatively low-leveled ninja, they can progress to become a Chūnin, by successfully completing the Chūnin Exams, a set of difficult tasks made to test the skills of Genin to see whether or not they should be Chūnin.
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Chūnin
Chūnin (中忍; Literally meaning "Middle Ninja", Meaning (Viz) "Journeyman Ninja") are ninja who are qualified to watch over and guide other ninja. Chūnin have reached a level of maturity that primarily consists of leadership skills and tactical prowess. This is because the genin who don't have the skills to become chūnin are weeded out in testing. Some of them, like Iruka Umino and Mizuki, function as Academy teachers and others, like Shikamaru Nara, serve as team leaders in charge of small teams who need to make decisions and utilize the skills of the shinobi under their command to the maximum effect. Chūnin are typically sent on C-rank or B-rank missions.
To become a chūnin, a genin participates in a large examination, known as the chūnin exams. The only exam seen in the series is a three-stage exam held in Konohagakure. Those who pass the test and become chūnin can wear an identifying flak jacket that holds ninjutsu scrolls. This vest is not mandatory; instead, some opt for more elaborate clothing like capes and robes.
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Tokubetsu Jōnin
Tokubetsu Jōnin (特別上忍, Tokubetsu Jōnin; English TV "Special Jōnin"; Literally meaning "Special High Ninja"; sometimes known as Tokujō for short) are ninja who, rather than all-around Jōnin training, have Jōnin-level ability in a single area or skill, much like warrant officers of real-world militaries. They are elite specialists in their areas and are often assigned as subordinates to regular Jōnin when their services are needed. One example of a Tokubetsu Jōnin would be Ibiki Morino, whose unique ability to completely understand the workings of the human mind makes him a Jōnin-level interrogation expert.
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Jōnin
Jōnin (上忍, Jōnin; Literally meaning "High Ninja", Meaning (Viz) "Elite Ninja") are generally highly-experienced shinobi with great individual skill who serve as military captains. They are often sent on A-Rank missions, and experienced Jōnin may even be sent on S-Class missions (which are considered to be the greatest difficulty). It is not unusual for Jōnin to go on missions alone. Jōnin are generally able to use at least two types of elemental chakra, some genjutsu, and above-average taijutsu skills.
It is as of yet unknown what one has to undergo to become one. It is mentioned in the Naruto Anime Profiles databook that Jōnin are appointed, however there was mention of a Jōnin exam in the anime's Kurama filler arc. When a ninja becomes a Jōnin, they may be assigned three Genin to look over. One part of their duties is to help instruct and train these Genin to become competent ninja.
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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. These teams are meant to give the new shinobi practical skills, while already being a productive member of the organization. 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 only exist for the duration of the mission, such as the Sasuke Retrieval Team, but in certain cases these teams are more organized and lasting, such as the Nijū Shōtai, created to battle the Akatsuki threat.
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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. This Head Ninja helps in leading the shinobi forces and is capable of representing the village. Konohagakure has the Jōnin Commander, who represents the regular forces in councils and likely helps in commanding them.
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ANBU
The ANBU (暗部, Dark Side), short for Ansatsu Senjutsu Tokushu Butai (暗殺戦術特殊部隊, Special Assassination and Tactical Squad; English Version: ANBU Black Ops), take orders directly from the Kage, performing special high-level missions, such as assassinations and torture. The ANBU usually work in teams formed to the requirements of the mission, ensuring maximum success. The shinobi in the ANBU are hand-picked by the Kage; chosen for their individual capabilities and special skills. Age, gender, background, or previous rank bear no weight in this decision.
There are apparently no true ranks within the ANBU, as is the case with the regular forces. Team leadership and hierarchy seem to be based on merit and experience. The leaders of the teams are called squad leaders (分隊長, Buntaichō), a position held in high regards.
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 group named Root would carry out extremely secretive missions and were not under the direct authority of previous Hokage.
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Medical Teams
The Medical Teams (医療班, Iryō-han) are the back-up of the shinobi forces. They consist of medical-nin, working behind the scenes to heal the sick and injured shinobi and to make sure the organisation is always in peak condition. Medical-nins are also similar to HM or Hospital Corpsman of the military in real life. They also do extensive research into new techniques, medicine, and into diseases and the human body. Although not seen very often, they are highly respected. Even to a jōnin, the advanced skills of these shinobi appear 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. However, back in the village, it is the Medical Teams who run the hospital and treat the wounded.