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The Foundation, also known as ROOT, is a Konohagakure ANBU training department founded by Danzo. They carry out missions that Danzo 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 acted in the dark.

Unlike normal ANBU, they carry a tipless Tanto instead of a Katana (however, Indo carries a katana). This is an extremely strict group, since Danzo has trained the members to lose their emotions. Each member has a codename; even the members themselves seem to not know their original names. It is unknown if Indo's nickname is "The Dark Ninja", for it is an alias given by Konohagakure.

Even after disbanding, the members remain loyal to Danzo, and retain their training of being emotionless to accomplish their objectives. Ind, however, has shown that he does want to work for Danzo.

Each member of the Foundation has a Cursed Seal imprinted on their tongue by Danzo, near the back of their throat, which will paralyze their entire body if they try to speak anything about Danzo, rendering them unable to speak or move; this is to prevent interrogations for information or betrayal. Indo has secretly had his removed by Semoiya Secoiya in Part 1. Sakura Haruno even noted that she felt this method is awful.

Indo Huiyo

Their member, Indo Huiyo, is secretly a member. However, he has been trained in the Ninja Academy as a Genin. In Part 2, Indo gets frustrated with Danzo, but agrees to his mission. Danzo questions Indo's loyalty to the Foundation since.

Missions

Kill Sasuke Uchiha

Danzo told Indo to eliminate Sasuke Uchiha for his defection. Even though Indo agreed, he hasn't done so yet.

Crushing the Ame Rebels

  • Assigned to: Presumed all
  • Outcome: Failure

Danzo made an alliance with Amegakure's leader, Hanzō, to help him crush the rebel group led by Yahiko. In turn, Hanzo would help Danzo become Hokage. He helped him capture Konan, and both of them forced Nagato to choose who would die. In the end, Nagato killed all the Foundation members there in his rage.

Kill the Hannya Assassins

  • Assigned to: Unknown
  • Outcome: Success

Danzo once ordered the assassination of the Hannya Assassins of the Land of Wood. The order was apparently successful, but according to Fū and Torune, remnants still exist and target Foundation.

Infiltrating Orochimaru's Hideout

  • Assigned to: Sai
  • Outcome: Failure

Danzo 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 Danzo's behalf. He offered to have the Foundation 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 Danzo had branded as a traitor. Sai, having befriended teammate Naruto Uzumaki, was later unwilling to complete this task, resulting in the failure of his mission.

Conquering Konoha

  • Assigned to:  All (except Indo Huiyo)
  • Outcome: Pending success; Danzo made acting Hokage

During Pain's attack on Konoha, Danzo kept the members of the Foundation from helping in the village's defense, hoping that Pain's actions would allow him to take the title of Hokage. Following the Invasion, Danzo 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.

Observing Naruto

  • Assigned to: Sai, Others
  • Outcome: "Ongoing"

After Danzo is elected by the Fire Daimyo 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 Danzo still requires the votes of the Jonin 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, he has betrayed Danzo and helped Naruto escape.

Tracking Anko

  • Assigned to: Dajimu and Tera
  • Outcome: Ongoing

While Anko is still on the mission to find and capture Kabuto, Danzo sends two of his men, Dajimu and Tera, to trail Orochimaru's former student. However, with the current situation of Konoha, Danzo orders his men to wait with getting rid of Anko, preferring to focus on finding Kabuto before she does.

Tracking Kabuto

  • Assigned to: Terai
  • Outcome: Ongoing

Because Kabuto might know about Danzo's involvement with Orochimaru, and because Kabuto's medical expertise could be used to heal his right arm and eye, Danzo orders his men to find Kabuto, leaving the mission in Terai's hands despite the village being on lockdown due to the Kage Summit.

Watch Sai and Naruto

  • Assigned to: Two unknown members
  • Outcome: Failure

Fearing Sai's loyalty to him, Danzo assigned two Foundation members to watch Sai as he watches Naruto. However, Konohamaru and Kakashi Hatake help Naruto escape to the Kage Summit and make it seem Sai is still loyal to Danzo.

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Protecting Danzo

  • Assigned to: Fū and Torune
  • Outcome: Ongoing

As Danzo is preparing to attend the Kage Summit, he is made aware of the order to bring two bodyguards with no exceptions. He chooses Fū and Torune because they are the top two members of the Foundation. Torune is 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.

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