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 Madara Uchiha (うちはマダラ, Uchiha Madara) is a major antagonist of the series. He co-foundedKonohagakure and Akatsuki, and was once the leader of the Uchiha clan.^[3] When first introduced, he poses as Tobi (トビ), Deidara's partner in Akatsuki.He was also once Mizukage of Kirigakure.

Madara had mastered his Sharingan at a young age, and received praise for that. Even after being scarred by Hashirama Senju and losing a great amount of power, his Sharingan can still see the color of chakra, as he saw the Poisonous Nano Bugs Technique spreading through Fū.^[19] Due to his mask covering the left side of his face, Madara only has been shown with his right Sharingan.

 Nagato (長門), better known as Pain (ペイン, Pein), was the recognized leader of Akatsuki andAmegakure and was a major antagonist in the series. Referred to as "Leader" by all Akatsuki members, except for Konan, he directed the actions of the rest of the members and maintained authority over them. However, he had secretly collaborated with Tobi,^[3] who was actually Madara Uchiha, the benefactor of Akatsuki.

 Konan (小南) was the only kunoichi in Akatsuki, and the partner of Nagato, being the only member to call him by his name. She is now the current leader of Amegakure.

Konan is an S-Rank kunoichi and her skills were held in high regard by her partner, Pain, although Jiraiya held her off with relative ease. She has an amazing natural talent for origami,^[4] as seen with the paper flower she keeps in her hair. As a child, after training with Jiraiya, she was able to form paper weapons infused with her chakra.

 Itachi Uchiha (うちはイタチ, Uchiha Itachi) was Sasuke Uchiha's older brother, an S-class missing-nin from Konohagakure and a prominent member of Akatsuki who was partnered with Kisame Hoshigaki.

Itachi was a master of all the Uchiha clan's techniques, along with the Sharingan, and had great prowess with all of the three main types of jutsu.

 Kisame Hoshigaki (干柿 鬼鮫 Hoshigaki Kisame) is a former ninja of Kirigakure and partnered to Itachi Uchiha, having a unique appearance with pale blue skin, a gill-like facial structure, and sharp triangular teeth. While most Akatsuki partners are hostile towards each other, Kisame and Itachi get along considerably well; Kisame does as Itachi asks of him unquestioningly and always looks out for Itachi's well-being. While he was still loyal to Kirigakure, Kisame was one of the Seven Swordsmen of the Mist, a group of violent ninja that use particularly large swords in battle. His sword, Samehada is a living weapon covered in scales that can absorb untold amounts of an opponent's chakra. Only allowing those it sees as worthy to wield it, Samehada can provide the user with the chakra it holds, ensuring him an infinite amount of stamina

 Zetsu  is the only member of Akatsuki to regularly act without a partner. This is in part a result of his ability to merge with any object and quickly travel to a new location, something that few other ninja are capable of. Because of this ability Zetsu serves a variety of different positions in Akatsuki, such as a spy that observes and reports on battles of interest or a lookout during Akatsuki's meetings. He is cannibalistic, and is often sent to dispose of bodies Akatsuki does not want found, mirroring the large venus flytrap that envelops his body. Zetsu's body is split into two different colors, his right side being black and his left being white. Similarly, the two sides have their own personalities and knowledge bases, frequently leading to discussions and arguments between the two. If necessary, the two halves can split apart and act independently.

 Deidara is a former ninja of Iwagakure, and was also a terrorist bomber-for-hire before Itachi Uchiha forced him to join the Akatsuki. Though he came to embrace the organization, Deidara holds a grudge against Itachi and all Uchiha throughout the series, as he feels their Sharingan eyes look down on his abilities. Upon joining the Akatsuki, he is partnered with Sasori, whom Deidara treats as his superior due to his artistic expertise. Sasori is replaced by Tobiafter his death, and Deidara assumes the master-position as Sasori had before him. Though he abuses Tobi when he annoys him, Deidara becomes more like a teacher to Tobi, and adopts a genuine care for his well-being. Each of Deidara's hands have mouths on them that, by infusing clay or other fine-grained minerals with chakra, create "sculptures" that are actually bombs that explode with varying intensities.

 Kakuzu (角都) is the partner of Hidan and a former ninja of Takigakure, the Village Hidden in a Waterfall. Kakuzu is motivated by greed and joins the Akatsuki to seek out valuable bounties. However, his extreme temperament led Kakuzu to dislike having a partner and eventually killing whoever he is partnered with in a fit of rage, being paired up with the immortal Hidan as a result. Kakuzu's body is composed of large amounts of black threads, allowing him to reattach any bodypart, his or another, back onto its owner. The threads are also capable of piercing flesh, which Kakuzu uses to remove the still-beating hearts of his opponents for his personal use while executing a forbidden Jutsu called Jiongu to integrate their hearts into his body to cheat death and extend his life indefinitely.Claiming to have lived since the time of Hashirama Senju, Kakuzu can store up to four spare hearts in animal masks that are sewn to his back. The masks can be detached during combat situations to shoot elemental blasts at his opponents, and can quickly be recalled to his body if he needs a replacement heart.

 Hidan (飛段^?) is the immortal, foul-mouthed, and masochistic partner of Kakuzu and a former ninja of Yugakure, the Village Hidden in the Steam. He is a member of the Jashin (ジャシン^?, lit. "evil god") religion, a religion that worships a deity of the same name and where wreaking anything less than death and utter destruction in battle is considered a sin. His religion's experimentations have led to the creation of his unique abilities; by consuming an opponent's blood and then drawing Jashin's triangular-design on the ground, Hidan can create a voodoo doll-like link with his opponent. Once this link is created, any damage done to Hidan's body is reflected on his opponent, allowing him to kill them by giving himself fatal injuries. Because he is immortal, Hidan is not impaired while doing this, instead finding pleasure in the pain it causes him.

 Sasori (サソリ) is a former ninja of Sunagakure and known as "Sasori of the Red Sand" (赤砂のサソリ Akasuna no Sasori). His parents died when he was young, leaving him in the care of his grandmother, Chiyo who taught Sasori the art of puppetry, which he refined to fit his needs over the years. Lacking the love of parents, Sasori left Sunagakure when he got older and joined Akatsuki where he is initially partnered with Orochimaru. After Orochimaru's defection Sasori teamed withDeidara, who looks to him and his artistic knowledge with reverence. In due time he devised a way to convert the corpses of humans into puppets, allowing him to use any of the ninja abilities they possessed during their life for himself. In time he even converted his own body into a puppet, which essentially gives him eternal life and allows him to control hundreds of puppets at once.