Essential to even the most basic jutsu, chakra is a mixture of the energy present in every cell of the body and the spiritual energy gained from exercise and experience. Once mixed, it can be channeled through the chakra circulatory system, which is to chakra as the regular circulatory system is to blood, to any of the 361 chakra points (called tenketsu) in the body. Through various methods, the most common of which is hand seals, the chakra can then be manipulated to create an effect that would not be possible otherwise, such as walking on water.
By mixing different ratios of the two energies, new types of chakra can be formed. The most common product is elemental chakra, which is used to perform elemental jutsu. Most ninja have a natural affinity to one type of chakra, but they have the capacity to create elemental chakra apart from their own affinity. There are six basic elements, each stronger and weaker to another; five have been shown so far, but their relations, weaknesses, and strengths to each other are all explored with the unnamed sixth seemingly skipped. In addition to these six elements, certain kekkei genkai can mix elemental chakra to form new elements, such as ice (wind and water), wood (earth and water) and lava (earth and fire). While many ninjas can use more than one type of chakra, they cannot use them simultaneously.
Normal chakra is a form of energy all living individuals naturally produce to some degree. Contained in the "chakra coils" that mainly surround and connect to each chakra-producing organ, the energy circulates throughout the body in a network called the "chakra circulatory system" (similar to the cardiovascular system). Certain groups, such as ninja, have learned to generate more chakra and release it outside their bodies through their "chakra points" (tenketsu) in order to perform special techniques (jutsu). Chakra is not normally visible to the human eye, though chakra can be seen in situations where a person releases as much of their chakra as possible. This is rarely seen due to the restrictions of certain chakra points (Eight Gates), limiting the amount of chakra an individual can release at a single given time. Chakra can also be visible when doing a specific jutsu (such as the Rasengan and the Chidori) which take a high degree of chakra control to perform.
Out of the many different types of jutsu, ninjutsu, genjutsu, doujutsu, and so on, all require the use of chakra. However, taijutsu is different, usually requiring no chakra use whatsoever. Stamina is all that is needed. While the ninja still needs a set amount of chakra to live (i.e. life force energy), regular taijutsu doesn't require any active molding or manipulation of chakra (with few exceptions). A standard attack like a punch or kick falls into this jutsu category.
Chakra is the resulting form of energy when two other forms of energy are mixed together. The two energies are referred to as "physical energy" and "spiritual energy." Physical energy is collected from the body's cells and can be increased through training, stimulants, and exercise. Spiritual energy is derived from the mind's consciousness (i.e. the soul) and can be increased through studying, meditation, and experience. Having these two energies become more powerful will in-turn make the created chakra more powerful. Therefore, practicing a jutsu repeatedly will build-up experience, building up one's spiritual energy, and thus allowing more chakra to be created. As a result, the ninja is able to do that same jutsu with more power. This same cycle applies for physical energy, except this time, instead of doing things like meditation, the ninja could, say, do push-ups.
The general term for the source of chakra, the overall physical and spiritual energy a person has, is "total stamina". The maximum amount of chakra an individual can create and release at a single given time is called the person's "chakra capacity."
In Naruto, chakra takes time and lots of training to gradually build up. So what's really the key is not actually having chakra, but being able to sufficiently control it. Everyone has chakra, but only skilled ninja can correctly "mold" and "manipulate" it to its fullest extent.
Molding chakra means to extract energies from both the body's cells and the mind's consciousness, then mixing them together within the individual. The amount of each energy will differ from the type of technique the ninja wishes to execute. In other words, a ninja could create too much or too little chakra for a given jutsu, and the chakra cannot be used efficiently. In addition, even if a ninja is able to mold the correct amount of chakra, if they aren't able to manipulate the chakra properly, the desired jutsu won't be as effective or not executed at all. Wasting energy will create a weakness of not being able to fight for a long period of time.
As an in-between stage, some ninja can partially control their chakra. This means they can use their chakra, but not effectively control it, which results in a poorly executed jutsu, and more importantly, running out of chakra early in a fight. To manipulate their chakra more easily, hand seals can be used. With these hand seals, users can control their chakra with higher efficiency, allowing them to execute their jutsu more effectively. Different jutsu require different hand seals.
When creating a ninjutsu, the two methods of manipulating chakra are referred to as "Nature Transformation" and "Shape Transformation":
Nature Transformation usually deals with changing the nature of normal chakra into an element. There is also the Nature Transformation of Yin and Yang, but little is known about this.
Shape Transformation deals with controlling the form and potency of chakra.
These two methods can be implemented separately or together in order to create a ninjutsu.
The general term for the exact molding and proper manipulation of chakra is "chakra control."
Based on which ninjutsu the ninja uses, the amount of chakra will be different, as would the element the ninja employs. The five main elemental types are also the names for the Five Great Shinobi Nations: Fire, Wind, Lightning, Earth and Water. Each ninja has the potential to better utilize one of these styles and potentially more. Rinnegan users somehow has the ability to control all five elements.
Advanced elements such Wood Release and Ice Release are created of combining different elemental chakra types. Doing this is only possible with a kekkei genkai in canon. However, the first movie has shown that shinobi of the Land of Snow are able to perform Ice Release techniques without a bloodline by manipulating the ice around them. Furthermore, in the Flower country filler arc Renga was able to use Ice Release without an ice source or kekkai genkai.
In the Naruto world, there are nine tailed beasts, which are ancient demons with immense chakra. In fact, they are malevolent concentrations of chakra that have taken on a corporeal form (mind and body). During the Great Shinobi Wars, each country's Hidden Village tried to make use of the tailed beasts for military purposes and competed for them. However, no one was ever able to truly bring the tailed beasts under control. The only way to partially control them is to seal them within a human with powerful sealing techniques. The hosts of the tailed beasts are called jinchūriki.
The jinchūriki can tap into the tailed beast's chakra for his or her own power. However, using such chakra can be harmful to the jinchūriki, with the host's body and mind being influenced or even taken over by his or her demon. In the case of Naruto Uzumaki, when he uses the Nine-Tailed Demon Fox's chakra and reaches his four-tailed transformation, the chakra is so concentrated around his body that it constantly burns and repairs his body right away, shortening his lifespan. Tapping into such unnatural chakra is very harmful to the host, as the host's personality gets suppressed by the animalistic blood lust of the tailed beasts and the intensity of chakra will harm the host if used for extended periods of time.
Senjutsu Chakra, the chakra needed to perform senjutsu, is chakra that contains the energy found in nature itself. It's a powerful source of energy, able to grant a ninja increased strength, speed, and endurance for taijutsu, as well as enhancing the power of one's ninjutsu and genjutsu. Sage chakra is created through the three-way mixing and balancing of one's physical energy and spiritual energy, as well as the natural energy from the atmosphere/air and terrain/ground. Since the three energies need to be equally balanced, the higher one's personal chakra capacity (physical energy and spiritual energy), the more natural energy they can add to the mix. Only those with a large chakra capacity can gather the natural energy needed for entering a powerful state called Sage Mode. Also, only when a person remains "perfectly still," no longer disrupting the flow of nature around them like ripples in a pond, can they properly feel and harness natural energy. Remaining completely still for a period of time takes a great deal of concentration and patience, requiring a highly motivated state of mind.
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