Root

is a Konohagakure ANBU subdivision founded by Danzō Shimura. They carry out missions that Danzō believes will benefit Konoha, at least some of which are less than respectable. The organization's top priority is its secrecy, and most of its missions are carried out in the dark. Root was officially disbanded at some point in the past, but remains active 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 group, and Danzō has trained its members to lose their emotions by growing up as brothers from a young age, then later made to kill each other so that their emotions would be destroyed; this method was extremely similar, if not the same, as Kirigakure Academy's former graduation test. Each member has a codename; even the members themselves seem to not know their original names. Unlike normal ANBU, they carry a tipless tantō instead of a katana.

Each member of Root has a cursed seal imprinted on their tongue by Danzō, near the back of their throat, which will paralyze their entire body if they try to speak anything about Danzō, rendering them unable to speak or move; this is to prevent interrogations for information or betrayal. The seal disappeared after Danzō's death.

Crushing the Ame Rebels

 * Assigned to: Presumed all
 * 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 forced 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.

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.

Conquering 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 defense, 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: Ongoing/Failure

After Danzō is elected by the Fire Daimyō to be acting Hokage, he orders Sai to keep an eye on Naruto, 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 favor). However, Sai betrays Danzō and helps Naruto elude surveillance.

Tracking Anko

 * Assigned to: Dajimu and Tera
 * Outcome: Failure

While Anko 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, 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 organization. However, both of the bodyguards were teleported away by Madara Uchiha 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 organization appears to have come from Danzō's view of himself towards Hiruzen. Seeing Hiruzen as the leaves that bask in the sunlight, and himself as the "roots" that grow in the dark.