Naruto: Root, Explained

Danzo’s secretive Root organization emerged from the shadows. How far would they go for the sake of Konohagakure?


  • Root, led by Danzō Shimura, carried out extreme, secretive missions for Konoha’s benefit.
  • Root members faced intense training, brainwashing, and loyalty solely to Danzō even after his death.
  • Sai, an elite Root member, overcame emotionless conditioning and formed bonds after joining Team Kakashi.

The hidden village of Konohagakure is renowned for its elite forces, from the revered Hokage down to the masked Anbu Black Ops, who operate in secrecy. However, even among these covert units, one group stood out for their extreme tactics and unwavering dedication—Root.

Led by the ambitious Danzō Shimura, Root took the ideals of serving Konoha’s interests to their darkest extremes. Through infiltration, assassination, and manipulation, they fought to strengthen the village from the shadows. But their methods would plunge them into controversy and lead to their downfall. Let’s take a deeper look at this shadowy organization and its role within the Naruto world.

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Origin and Leadership of Root


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Danzō Shimura

Root was a secretive branch of Konohagakure’s Anbu training subdivision that was led by Danzō Shimura. Its core purpose was to carry out missions that Danzō believed would benefit Konoha, even if the methods used were less than respectable. As the organization viewed itself as “the unseen ones who support the great tree of Konoha from the depths of the earth,” some missions involved eliminating individuals considered potential threats merely for expressing dislike for the village without having actually done anything against it.

Maintaining utmost secrecy was Root’s top priority, and most missions were conducted autonomously without Konoha’s authority and in the dark. While officially disbanded after Danzō led the Uchiha clan’s downfall, Root remained active as an underground organization until Danzō’s death. Despite orders from the Third Hokage to disband, Root members remained loyal solely to Danzō’s commands over even the Hokage’s. Following Danzō’s death, when Root’s clandestine actions were revealed, members like Tanuki Shigaraki were exiled as outcasts.

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However, after the Fourth Shinobi World War, Tsunade and Kakashi prevented thorough background checks in a bid to shield Root members from further ostracization. This allowed some, such as Kido Tsumiki and Magire, to integrate into the regular Anbu forces. Yet due to the lack of investigations, Tanuki Shigaraki’s daughter Sumire was able to infiltrate Konoha, seeking revenge for how the village shunned Root remnants. Upon Danzō’s demise, Sai aimed to help former members break from his dark influence.

Root’s training methods


Root members underwent an extremely rigorous and secretive training regiment. Each member had a cursed seal imprinted on their tongue by Danzō. This seal was meant to ensure total secrecy and prevent leaked information even under torture. If a Root member spoke about Danzō or the organization, the seal would activate and paralyze their entire body, rendering them unable to speak or move.

In addition to the seal, Root members were trained to eliminate all emotion. Danzō had the members grow up as brothers from a young age, only to later make them kill one another. This cruel method was used to destroy any sense of attachment or sentiment between the members. It closely mirrored the former graduation test at Kirigakure Academy, which was notoriously harsh.

Emotions lead one to hate… and hate leads one to conflict and war…

Root operatives were known only by their codenames, even to each other. They did not know their original names. Unlike regular Anbu, Root members carried a tipless tantō sword instead of a traditional katana. They also only took orders from Danzō and followed his commands above even the Hokage, unless specifically told otherwise.

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Long-term brainwashing was another specialty of Root’s training. For example, one member named Nonō Yakushi was unwittingly brainwashed through a photo series that initially showed her former ward Kabuto as a child, but slowly switched to a different person entirely. Root then instructed her to kill the real Kabuto, resulting in her failure to recognize him during their confrontation due to the effective psychological conditioning.

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Most Infamous Member: Sai


Sai was a highly skilled shinobi who was among the strongest members of the secret Anbu Root branch. After being orphaned at a young age, he was recruited by Danzō Shimura, and underwent intense conditioning to remove all emotions and personal connections. Though successful, Sai retained an interest and talent in art, which was encouraged by his adoptive brother Shin. Unfortunately, the final stage of Root’s training required Sai and Shin to fight to the death, though Shin died of an illness before that could occur.

As a Root member, Sai carried out numerous assassinations of those deemed threats to Konoha, demonstrating his deadly combat abilities. After being assigned to Team Kakashi, Sai began to rediscover his empathy and form personal bonds, eventually leaving behind his emotionless root conditioning.

Other notable Root members:

  • Yamato: The only member that Danzo personally trained himself.
  • Kabuto Yakushi: Infiltrated several villages as a spy for Root at a young age.
  • Nono Yakushi: A skilled intelligence gatherer who infiltrated Iwagakure for Root.
  • Fū: One of Danzo’s bodyguards during the Five Kage Summit.
  • Torune: The other bodyguard alongside Fū. Later joined the Anbu forces after the disbanding of Root.

The missions of Root

Danzo's Root Anbu

Root carried out several classified missions on behalf of their leader, Danzō Shimura. One of their earliest missions was to create an ultimate weapon known as Gozu Tennō. Danzō harvested Hashirama Senju’s wood release cells and entrusted the member Tanuki Shigaraki with using them to create a giant chakra-harvesting yōkai. Though the project continued after Danzō’s death, ultimately resulting in Tanuki implanting it in his daughter to attack the village in revenge.

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A highly skilled spy, Nono Yakushi, was assigned to infiltrate Iwagakure and confirm intelligence about their potential plans to attack Konoha. Despite initially refusing due to leaving Root, she successfully penetrated Iwa’s defenses and remained there for years. Meanwhile, Kabuto carried out extensive espionage by infiltrating all five great villages over several years on Danzo’s orders.

Upon deeming Kabuto and Nono threats, Danzo hatched a plan to have them kill each other through brainwashing Nono. This led to her death at Kabuto’s hands and his allying with the traitor Orochimaru. Additionally, Root members disguised as Iwa ninja attacked border towns to frame them during peace negotiations. And Danzo manipulated the leader Hanzo to believe Akatsuki threatened his rule, resulting in an alliance to crush resistance, with Ame’s Root division being largely wiped out.

While some missions, like assassinating threats, were successful, others ended in failure or unexpected consequences. An attempt to help Hanzō destroy the rebellion led by Nagato backfired when Nagato wiped out their forces in revenge. Likewise, an effort to kill the Third Hokage was foiled thanks to a new member informing Hiruzen of the plan. Over time, Root took on more missions for Danzō but ultimately met their end with his death at the hands of Sasuke Uchiha.

Naruto is available to stream on Crunchyroll.

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A popular shonen anime based on Masashi Kishimoto’s manga, Naruto follows its eponymous shinobi’s journey as he goes from his town’s outsider to its hero.

Release Date

October 2, 2002




Masashi Kishimoto

Number of Episodes


Streaming Service(s)

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, Netflix

Watch on Amazon

Categorías: Anime

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