Root

is an officially disbanded branch of Konohagakure's Anbu training subdivision founded by Danzō Shimura. After his death, however, it is unknown what's become of the group.

Overview
Root carries out missions that Danzō believes will benefit Konoha. Because of its core views as "the unseen ones who support the great tree of Konoha from the depths of the earth", some of these missions may be less than respectable. The organisation's top priority is its secrecy, and most of its missions are carried out in the dark - autonomous of Konoha's authority. Root was officially disbanded at some point in the past, but remained active as an underground organisation until Danzō's death. It is unknown what will become of Root, but Sai suggests its members look to Kakashi Hatake for guidance since Kakashi, at the time, was slated to become Hokage.

Root is an extremely strict, and secretive group and as such each member of the organisation has a cursed seal imprinted on the back of their tongues by Danzō, which when activated, will paralyse their entire body if they try to speak anything about Danzō or the organisation, rendering them unable to speak or move. Sai noted that this was done in an effort to prevent information leak should any of them be captured and interrogated by enemy forces. The seal disappeared after Danzō's death.

Danzō has also trained its members to lose their emotions by growing up as brothers from a young age, only to later be made to kill each other. This is done to kill any sense of sentiment or emotional attachment. This method was extremely similar, if not identical, to the Kirigakure Academy's former graduation test. Each member has a codename; even the members themselves apparently do not know their original names. Unlike normal Anbu, they carry a tip-less tantō instead of a katana. Also unlike normal Anbu, members of Root take orders only from Danzō instead of the Kage, unless ordered to otherwise. Another speciality of the organisation was slow, long-term brainwashing. In the case of one of their members, Nonō Yakushi, she was brainwashed through a series of photographs starting with photographs of Kabuto — one of her former wards at orphanage showing him growing up. Eventually, they slowly switched the person in the photographs entirely and then gave her the order to kill the actual Kabuto. This resulted in Nonō not recognising the young man in their final confrontation.

Though the members wear the standard cloak and mask of the Konohagakure Anbu, they don't have an actual standardised uniform like the others. Underneath the cloak each Root member wears a personal attire. The only single distinguishing garment they all wear is a short, black, midriff jacket, with red straps over the shoulders along with the tip-less tantō.

Infiltrate Iwagakure

 * Assigned to: Nonō Yakushi
 * Outcome: Success

Danzō had Nonō who was regarded as an elite in the field of intelligence gathering, infiltrate Iwagakure in order to confirm intelligence they received that Iwagakure was planning to attack Konoha. Though she initially refused as she had left the organisation, she eventually accepted the mission. She successfully infiltrated the village and remained there for several years. She was critically wounded, however, after attacking Kabuto Yakushi whom had also infiltrated the village as a spy.

Infiltrate Great Hidden Villages

 * Assigned to: Kabuto Yakushi
 * Outcome: Success

Danzō had Kabuto placed into all the other Great Hidden Villages (and possibly other villages) over the course of a few years to spy on them for Root.

Assassinate Kabuto/Nonō

 * Assigned to: Nonō Yakushi, Orochimaru
 * Outcome: Failure/Partial Success

Viewing Kabuto and Nonō as a threat to Root, after they had become "too good" of spies, Danzō schemed to have both individuals kills each other. Slowly brainwashing Nonō, by gradually switching photos of Kabuto with pictures of a different person and saying it was him, Danzō revealed that Kabuto had joined Root for the orphanage's sake and told her that they would release him once she assassinated a certain person. Unbeknownst to her when she was carrying out this mission, she was attacking the real Kabuto. Ultimately, Nonō was cut down by Kabuto who fled after she didn't remember him. This mission culminated in Nonō's death and Kabuto allying himself with the traitorous Orochimaru, who had decided to defect from Root, but had originally claimed that he was sent to kill either Kabuto or Nonō, depending who survived the ordeal.

Incriminate Iwagakure

 * Assigned to: Unknown, Danzō lead this mission
 * Outcome: Partial Success

In the anime, Danzō, in an effort to obstruct peace negotiations with Iwagakure, sought to incriminate the village by having a number of Root members masquerade as Iwa shinobi and attack villages along the border of Amegakure.

Manipulate Hanzō into an alliance

 * Assigned to: Unknown, Danzō lead this mission
 * Outcome: Success

In the anime, Danzō, after witnessing the power of the Rinnegan and wanting to use it for his own agenda, manipulated Hanzō into believing that Akatsuki was out to take over leadership of Amegakure. He did this by presenting Hanzō with corpses which he claimed were members of Hanzō's own clan.

Crushing the Ame Rebels

 * Assigned to: Unknown
 * Outcome: Failure

Danzō made an alliance with Amegakure's leader, Hanzō, to help him crush the rebel group led by Yahiko. In turn, Hanzō would help Danzō become Hokage. Although the joined forces did succeed in orchestrating the death of Yahiko, the mission ultimately failed when Nagato, enraged by Yahiko's death, killed practically all of Amegakure's and Root's shinobi present. Only Hanzō was shown to have escaped.

Assassinate Hiruzen Sarutobi

 * Assigned to: Kinoe and several others
 * Outcome: Failure

In the anime, unable to tolerate Hiruzen's passive approach to governing Konohagakure, Danzō sought to eliminate him shortly after resuming his post following the death of the Fourth Hokage. His Root members were disguised as a foreign group. The plan failed before it even began as Kakashi Hatake — a new Root member — chose to inform the Third Hokage of the treason, taking the Third's place to lure out the assailants and consequently making Danzō power-hungry and amoral nature known.

Retrieve Kakashi Hatake's Sharingan

 * Assigned to: Kinoe and Kinoto
 * Outcome: Failure

In the anime, as the vision in Danzō's Sharingan began to deteriorate, he ordered Kinoe and Kinoto to retrieve a replacement. As taking one from an Uchiha at the time would incite both suspicion and possible repercussion, they were ordered to take the one implanted in Kakashi, as his bad reputation for killing friends and not being a member of the Uchiha would likely make blow back minimal.

Killing the Prajñā Group

 * Assigned to: Unknown
 * Outcome: Success

Danzō once ordered for the assassination of the Prajñā Group, an Anbu regiment from the Land of Woods. The mission was apparently a success, but according to Fū and Torune, remnants still exist and target Root.

Infiltrating Orochimaru's Hideout

 * Assigned to: Sai
 * Outcome: Failure

Danzō assigned Sai to Team Kakashi, which went on a mission to find Sasuke Uchiha. During the course of the mission, Sai approached Orochimaru, Sasuke's mentor, on Danzō's behalf. He offered to have Root aid Orochimaru in "destroying" Konoha. When Orochimaru accepted and took Sai back to his hideout, Sai's true mission began: to protect Konoha by killing Sasuke, whom Danzō had branded as a traitor. Sai, having befriended team-mate Naruto Uzumaki, was later unwilling to complete this task, resulting in the failure of his mission.

Assuming Leadership of Konoha

 * Assigned to: Presumed all (minus Sai)
 * Outcome: Failure; Danzō now deceased

During Pain's attack on Konoha, Danzō kept the members of Root from helping in the village's defence, hoping that Pain's actions would allow him to take the title of Hokage. Following the invasion, Danzō was appointed as the acting Sixth Hokage, pending the vote of confidence. Sai was the only member known not to be among the group, as he was with Yamato and Anko Mitarashi, who were hunting down Kabuto Yakushi. The mission failed, as Danzō was ultimately killed by Sasuke Uchiha prior to achieving the title of Hokage.

Observing Naruto

 * Assigned to: Sai
 * Outcome: Discontinued since Danzō's death.

After Danzō is elected by the Fire Daimyō to be acting Hokage, he orders Sai to keep an eye on Naruto Uzumaki, and anything out of the ordinary is to be reported at once. This is because Danzō still requires the votes of the jōnin to be officially Hokage, and that he needs to keep Naruto, who is now considered a hero of the village, in check due to his status as a Jinchūriki (without doing anything to Naruto that may cause himself to lose favour). However, Sai betrays Danzō and helps Naruto elude surveillance.

Tracking Anko

 * Assigned to: Dajimu and Tera
 * Outcome: Failure

While Anko Mitarashi is still on the mission to find and capture Kabuto Yakushi, Danzō originally sent two of his men, Dajimu and Tera, to trail Orochimaru's former student. However, with the current situation of Konoha, Danzō ordered his men to not get rid of Anko, preferring to focus on finding Kabuto before she does. This failed, as Kabuto captured Anko and carried her off to a different location.

Tracking Kabuto

 * Assigned to: Terai
 * Outcome: Failure

Because Kabuto might know about Danzō's involvement with Orochimaru, and because Kabuto's medical expertise could be used to heal his right arm and eye, Danzō orders his men to find Kabuto, leaving the mission in Terai's hands despite the village being on lock-down due to the Kage Summit. Danzō was killed before Kabuto could be useful to him.

Watching Sai and Naruto

 * Assigned to: Two of Torune's unnamed subordinates
 * Outcome: Failure

Fearing Sai's loyalty to him is wavering, Danzō assigns two Root members to watch Sai as the latter watches Naruto. However, Kakashi Hatake and Konohamaru Sarutobi help Naruto escape to the Kage Summit and make it seem that Sai is still loyal to Danzō.

Protecting Danzō

 * Assigned to: Fū and Torune
 * Outcome: Failure

As Danzō was preparing to attend the Kage Summit, he was made aware of the order to bring two bodyguards with no exceptions. He chose Fū and Torune because they were the top two members of Root. Torune was also instructed to assign his men to keep an eye on Naruto, and to prevent him from leaving the village, just in case Sai would betray the organisation. However, both of the bodyguards were teleported away by Tobi and Danzo was struck in the heart by Sasuke Uchiha's Chidori Sharp Spear, mortally wounding him.

Recover the Byakugan

 * Assigned to: Fū
 * Outcome: Failure

As Ao trailed Danzō for betraying the Kage, Danzō ordered Fū to retrieve the Byakugan he possessed. Fū made a valiant effort to retrieve "Konoha's property" for Danzō but the Fifth Mizukage arrived and saw through Fū's trap causing Fū to fail.

Trivia

 * The name for this organisation appears to reflect Danzō's last words: "…you are the leaves bathing in the sun. I am the roots that grow in the dark."
 * Unlike other Root members' pair of black gloves, the ones worn by Sai leave both his index fingers and thumbs bare — a feature probably intended to favour the use of his drawing abilities.
 * The members of Root seemingly do not have the traditional Anbu tattoos branded on their shoulders.
 * The creed of this group may possibly be "In Root, you have no name. You have no feelings. You have no past. You have no future. There is only the mission." As recited by Sai and Hyō.
 * In Naruto: Shippūden episode 317, Danzō is revealed to recruit Root members himself, without the Hokage's interference. He favoured those from clans who possess special techniques, such as the Aburame, Yamanaka, and Uchiha clan. Interestingly enough, those who are selected don't go through the traditional training that requires them to kill their team-mates.