Missing-nin

are ninja who left their village without the intention of returning and severing ties with said village, often because they have committed criminal acts or to pursue other personal agendas; although this depends on the said ninja's intents, as Tsunade and Shizune left their village for many years without returning, yet not classified as runaways as they departed without ill-intentions. The ninja village that they are from will often try to track them down and eliminate them. This is not only done as a punishment for treason, but also to protect the secrets of the village, since it is possible to learn some of the village's techniques from the autopsy of their users. Kirigakure has a special hunter-nin task-force whose only objective is killing traitorous ninja.

Itachi Uchiha became a missing-nin based on the orders of his village's elders, in order to prevent a revolution that would be the foundation of a world war, and to infiltrate a criminal organisation. Due to the secretive truth of his criminal actions, the rest of the world believed that Itachi was a genuine criminal. This is an example of how some villages would sacrificially order their own soldiers to become renegades for what they believe to be the greater good.

Depending on the village leader's decisions, the missing-nin in question may be given leniency. The most prominent example is Sasuke Uchiha, who is not marked for death by the Fifth Hokage, Tsunade, as a favour to Naruto Uzumaki, and is instead to be brought back as a Konohagakure citizen. However, according to Kakashi Hatake, a missing-nin is typically marked for death simply for defecting, and such mercy is rare. Later, when Sasuke infiltrated Kumogakure and attempted to abduct their Eight-Tails' jinchūriki, Killer B, then attacked the Kage Summit, the pardon Tsunade granted him was nullified and the Five Kage elevated his status to an international criminal, meaning that he became a global-scale missing-nin. Eventually, however, due to Sasuke's assistance in the Fourth Shinobi World War and his willful surrender, he was given a second pardon by the Sixth Hokage, Kakashi; were it not for the former, he would have been sentenced to life in prison even had he not resisted arrest.

The ninja organisation Akatsuki is composed mostly of S-rank missing-nin, except for Nagato and Konan, who are the leaders of Amegakure. Most of the missing-nin throughout the series are antagonists. Several missing-nin continue to wear their forehead protector, while others may discard them. Akatsuki members who do retain their headbands carve long, horizontal scratches across the symbol, to show they have rescinded their allegiances and rejected their villages. The Bingo Book contains information on every missing-nin and is given to every jōnin and Anbu member by their respective Kage.

Due to the potential prejudice and intense power gifted, jinchūriki are feared for possibly turning on their respective villages. To prevent that, they are traditionally chosen relatives of a Kage, to reinforce their ties and loyalty to the village.