Root

Biodata

Feature	Value
Name	Root
Alias(es)	ANBU Root; “the darkness of the Hokage”
Affiliation	Konohagakure (formerly clandestine); commanded by Shimura Danzō
Occupation/Role	Covert intelligence, surveillance, infiltration, assassination, political manipulation, human experimentation, and evidence suppression
Status	Formally dismantled. Danzō was executed after Root's crimes were publicly exposed, and its last organized remnant base was purged. However, scattered former operatives, legacy files, surveillance rosters, and networks tied to Root continue to be exploited by figures such as Gray Crow and members of Konoha's old faction. 64 65 88 121 134
First Appearance	Chapter 1

Background / History

Root targeted nine-year-old Uchiha Shingetsu shortly after his transmigration, classifying the orphan as having “low recovery value” and seeking to take him as a sample. Its operatives possessed detailed information on his family status, unawakened Sharingan, chakra level, and residence. Two Root ninja were killed during the attempted abduction. 1 3

The organization continued to monitor Shingetsu after he awakened and rapidly developed his Sharingan. Danzō ordered surveillance, an apparent “accident” to test Shingetsu’s abilities, and the acquisition of a blood sample for research. 10 20

Root infiltrated the Uchiha compound through direct surveillance, eavesdropping talismans, a secret tunnel, tracking devices, and an embedded agent, Uchiha Shinsuke. Shingetsu’s countermeasures exposed these operations and gave the Uchiha Police Force grounds to pursue Root’s involvement publicly. 21 25 35 40

After a Root liaison was captured with a Root mark and duplicate Hokage deployment document, Root’s activities became a public scandal. Danzō attempted to suppress testimony with a tongue curse seal and later framed Root’s actions as unauthorized conduct by former members. 40 44

A destruction order intercepted by Shingetsu led the Uchiha Police Force and ANBU to raid a Root outpost. Recovered evidence included surveillance files, Sharingan-preservation fluid, lists of missing Uchiha, and the Night Owl Plan, an Uchiha elimination plan. 44 47

The Third Hokage suspended Root’s operational authority and ordered its strongholds taken over. Root responded by triggering self-destruct mechanisms and evacuating personnel and evidence from multiple sites. 47 Following further revelations tied to Danzō’s human experimentation, Root was sealed off, while Danzō became an A-Rank Missing-nin. 51 53

Danzō escaped Konoha with four surviving Root operatives and later cooperated with the Masked Man to fabricate evidence that the Uchiha had controlled the Nine-Tails. The Uchiha intercepted and recorded their discussion, leading to Danzō’s recapture, public exposure, elevation to S-Rank traitor status, and imprisonment for interrogation. 58 60

During Danzō’s interrogation, Shingetsu’s Mangekyō Sharingan exposed Root’s wider crimes: systematic Sharingan collection, orphan brainwashing, First Hokage-cell experimentation, surveillance of Konoha’s major clans, and a surviving remnant base beneath Old Mine Town. The latter was commanded by Owl and maintained the Konoha Purification Plan, which aimed to strike the Uchiha compound, Hokage Building, and the Nine-Tails jinchūriki’s residential district. 61 63

A joint Konoha force destroyed the Old Mine Town base after Shingetsu severed its remote detonation chains. Seven child test subjects were rescued, Owl was captured, and Root’s final laboratory records—including Wood Style experiment files and an outline of its brainwashing methods—were seized. Danzō was subsequently executed, and the twenty-three recovered Sharingan were returned to the Uchiha clan for memorial rites. 64 65

Although Root’s organized structure was destroyed, its methods and legacy continue to destabilize Konoha. Former Root operatives spread anti-Uchiha and anti-Naruto rumors under the direction of the unidentified Gray Crow, while Root-related archives, surveillance rosters, and old political dealings have become targets for Black Zetsu and Konoha’s remaining old faction. 88 95 98 121 134

Operations and Methods

Surveillance and infiltration

Root conducted long-term surveillance of the Uchiha clan and targeted Shingetsu personally.

• Used an underground tunnel on the perimeter of the Uchiha compound to infiltrate and observe the clan grounds. 23 25
• Planted Eavesdropping Talismans inside Shingetsu’s residence. 21 23
• Used tracking needles and chakra-sensing tags to monitor Shingetsu’s chakra use and Sharingan activity. 38
• Maintained agents and contacts within the Uchiha, including Uchiha Shinsuke. 35 37
• Possessed detailed intelligence files on potential targets, including Shingetsu’s personal circumstances and chakra assessment. 1 12
• Compiled long-term surveillance lists on the Uchiha, Hyūga, Nara, Yamanaka, Akimichi, Aburame, Inuzuka, and even members of the Sarutobi clan. 46 62
• Maintained surveillance rosters tracking the movements and combat strength of Uchiha leadership figures, including Fugaku, Shisui, Itachi, and Shingetsu. 134

Abduction and experimentation

Root treated Uchiha as research material and sought their Sharingan.

• Classified Shingetsu as a recoverable “sample” and planned to abduct him due to his lack of relatives. 1
• Collected Uchiha eyes and kept Sharingan in preservation fluid and sealed containers. 2 46 48
• Maintained records of missing Uchiha clansmen whose eyes were likely seized by Root. 46
• Conducted illegal human experimentation connected to Danzō’s grafted First Hokage cells. 51 53
• Intended to retain “controllable young” and obtain “special bloodline samples” under the Night Owl Plan. 47
• Conducted First Hokage-cell experiments with Orochimaru, sacrificing numerous test subjects in pursuit of a viable Wood Style recipient. 62
• Operated a “New Generation Vessel Project” involving the imprisonment and experimentation of children; seven surviving child subjects were recovered from the Old Mine Town base. 64 65
• Prepared Uchiha Sharingan as transplant material for Danzō and Root Grade-A members, with Shisui’s right eye and Shingetsu’s eyes listed as special targets. 61

Secrecy and evidence destruction

Root relied on deniability, internal seals, scapegoats, and rapid disposal of evidence.

• Members carried no direct identifiers, while the organization used unmarked masks and ANBU-like methods. 1 3
• Used a tongue curse seal to prevent captured operatives from revealing information. 16 43
• Prepared to fabricate Cloud Village spies as scapegoats for the attack on Shingetsu. 15
• Issued destruction orders to burn mission records, experimental materials, and surveillance files when its outpost was exposed. 44 45
• Activated self-destruct procedures across several strongholds during the organization’s evacuation. 47
• Used underground incineration facilities to dispose of preserved bodies, experimental materials, and records during emergency evacuations. 44
• Ordered remnant personnel to burn documents and kill or abandon test subjects when the Old Mine Town base was exposed. 64
• Relied on suicide measures, including poison, to prevent captured leaders such as Owl from being interrogated. 64

Political manipulation

Root sought to deepen division inside the Uchiha clan while isolating Shingetsu.

• Spread praise for Shingetsu to push him into becoming a hardline symbol opposed to Fugaku and the Hokage Building. 29 30
• Used Shinsuke to criticize Fugaku and advocate for Shingetsu to lead an aggressive investigation. 35 36
• Attempted to exploit Uchiha radicals and internal hostility toward the village. 29 30
• Used a liaison and falsified Hokage deployment document to encourage conflict between the Uchiha and village leadership. 39 41
• Danzō and surviving Root operatives later cooperated with the Masked Man to fabricate signs of Nine-Tails chakra activity and blame the Uchiha for controlling a tailed beast. 58 60
• Root remnants continued to circulate rumors targeting Naruto and the Uchiha after Danzō’s death, operating through the alias Gray Crow. 88
• Root’s archives and old accounts remain useful tools for factions seeking to revive fear of the Uchiha or discredit them before Konoha’s leadership. 121 134

Internal control and indoctrination

Root stripped its operatives of individuality and treated them as expendable tools.

• Operatives were trained to suppress fear, attachment, and personal identity in favor of mission completion. 1 25 64
• The organization branded members with the Cursed Tongue Eradication Seal to prevent the disclosure of Root secrets. 16 42 43
• Maintained a brainwashing program for orphans and test subjects, the general outline of which was recovered from the Old Mine Town base. 62 65
• Used Root’s ideology of “purifying” or protecting Konoha to motivate remnants into terrorist operations against the village itself. 63 64

Known Personnel

• Shimura Danzō — Root’s leader; ordered surveillance, testing, sample collection, and efforts to eliminate Shingetsu. He was later suspended, exposed through Root evidence, designated a Konoha A-Rank Missing-nin, recaptured as an S-Rank traitor, and executed for his crimes. 10 20 47 53 60 65
• Crow — Root elite jōnin who guarded a Black Sealing Box containing Sharingan during the evacuation. 47 48
• Owl — Commander of Root’s final known remnant base beneath Old Mine Town and overseer of the Konoha Purification Plan. He was captured after attempting to kill himself with poison. 63 64
• Torune Aburame — Root operative ordered by Danzō to participate in the ambush on Uchiha Shisui for his Mangekyō Sharingan. 50 52
• Yamanaka Fū — Root operative ordered by Danzō to participate in the ambush on Uchiha Shisui. 50 51
• Uchiha Shinsuke — Uchiha Police Force outer member and Root-linked infiltrator used to spread divisive rumors inside the clan. 35 37
• Root liaison — Captured after meeting Shinsuke; bore a Root mark and carried a duplicate Hokage deployment document. 40 43
• Gray Crow — Unidentified individual or controller directing scattered Root remnants in the spread of rumors against Naruto and the Uchiha. 88 98
• Root attack team — Two operatives sent to abduct Shingetsu as a sample; both were killed. 1 3

Facilities and Assets

• Root strongholds — Hidden bases ordered sealed by the Third Hokage; several self-destructed or were evacuated after Root’s exposure. 47
• Southeast Outpost — Peripheral underground facility raided by the Uchiha Police Force and ANBU; held surveillance records, experimental materials, captives, and Uchiha-related evidence. 44 46
• Secret Uchiha-compound tunnel — An infiltration route containing ANBU-style seals and evidence of prolonged surveillance. 23 25
• Black Sealing Box — Root container guarded by Crow during the evacuation; held Sharingan. 47 48
• Night Owl Plan — Root document outlining an Uchiha priority-elimination operation, nighttime elimination, retention of controllable youths, and collection of special bloodline samples. It designated the Police Force leadership, Uchiha radicals, and Sharingan awakeners as priority targets. 46 47
• Core Laboratory and Sharingan caches — Root facilities and sealed repositories used to store stolen Sharingan, transplantation materials, human-experiment records, and related evidence. One recovered cache contained twenty-three Sharingan. 46 61 65
• Old Mine Town remnant base — Root’s final known organized stronghold, located beneath an abandoned mining town near the Land of Fire border. It housed experimental subjects, traps, laboratory records, and the Konoha Purification Plan. 62 65
• Konoha Purification Plan — A Root remnant contingency to remotely detonate Explosive Tag nodes at the Uchiha compound, Hokage Building, and the Nine-Tails jinchūriki’s residential district in order to create chaos and vindicate Danzō’s ideology. 63 64
• Legacy archives and surveillance rosters — Root-related records concerning the Uchiha, Orochimaru, village politics, and the movements of Uchiha upper ranks. These materials remain a source of danger after Root’s collapse. 121 134

Relationships

• Uchiha Shingetsu — Primary target and adversary. Root first attempted to abduct him as a sample, then monitored, tested, framed, and sought to eliminate him as his influence grew. Shingetsu ultimately exposed its bases, plans, experiments, and surviving remnant network. 1 20 25 29 47 63 65 88
• Uchiha clan — Subject of systematic surveillance, infiltration, eye collection, and the Night Owl Plan. Root’s crimes against the clan became the central cause of its public downfall. 23 25 46 47 61 65
• Uchiha Police Force — Investigative and combat opposition that exposed Root’s tunnel, agents, liaison network, and outposts. It later participated in the destruction of the Old Mine Town remnant base and Danzō’s public arrest. 22 25 36 44 47 60 63 65
• Uchiha Shisui — A special Sharingan target. Danzō ordered Root operatives to ambush Shisui and seize his Mangekyō Sharingan, but the operation failed. 50 52
• ANBU — Root shares methods and institutional origins with ANBU, but ANBU later participated in sealing Root facilities under the Hokage’s orders and in joint operations against its remnants. 23 45 47 63 65
• Third Hokage Sarutobi Hiruzen — Initially constrained Root indirectly, then suspended its operations and ordered its bases seized after the Night Owl Plan was exposed. He later authorized the public investigation, prosecution, and execution of Danzō. 24 44 47 60 65
• Shimura Danzō — Root’s commander, whose policies and crimes drove its conflict with the Uchiha. Even after Root’s formal collapse, he mobilized surviving operatives and its remaining assets to continue his campaign against the clan. 1 10 20 47 58 63 65
• Orochimaru — Collaborator in Danzō’s human experimentation. Root’s records documented their First Hokage-cell research and related experiments on children. 62 65
• Masked Man — Danzō formed a temporary alliance with the Masked Man after becoming a rogue ninja, using surviving Root operatives in a failed plan to frame the Uchiha through the Nine-Tails. 58 60
• Black Zetsu — Not a confirmed Root member, but an outside manipulator that has exploited Root remnants, old faction members, and Root-related archives to renew suspicion against the Uchiha and destabilize Konoha. 88 121 134
• Shadowbreaker Squad — The special task force formed to investigate the Nine-Tails Incident, Black Zetsu, the Hidden Mist control chain, and Root’s lingering threads, including Gray Crow. 95 98

Story Role / Major Arcs

• Attempted abduction of Shingetsu — Root’s attack awakens Shingetsu’s Sharingan and begins his direct conflict with Danzō’s organization. 1 3
• Uchiha investigation — Root’s suspected involvement turns Shingetsu’s assault into a broader dispute between the Uchiha and Konoha’s leadership. 4 12 16
• Compound infiltration arc — Root’s eavesdropping, tunnel, and tracking operations are uncovered, proving it has penetrated Uchiha territory. 21 25
• Public-opinion manipulation arc — Root uses Shinsuke and planted rumors to radicalize the Uchiha and make Shingetsu a target. 29 40
• Public exposure and outpost raid — The captured liaison and destruction order expose Root before Konoha; an outpost raid uncovers its crimes. 41 46
• Night Owl Plan and evacuation — The elimination plan forces the suspension of Root, prompting the organization’s coordinated retreat and destruction of its bases. 47
• Danzō’s initial fall — The exposure of Danzō’s First Hokage-cell experiments contributes to Root’s sealing and Danzō’s designation as a missing-nin. 51 53
• Fugitive conspiracy and recapture — Danzō and surviving Root operatives collaborate with the Masked Man to frame the Uchiha for Nine-Tails activity, but are ambushed by the Uchiha and exposed publicly. 58 60
• Old Mine Town purge — Shingetsu’s Mangekyō exposes Root’s final remnant base and the Konoha Purification Plan. The joint assault stops the planned bombings, captures Owl, and rescues seven child test subjects. 61 65
• Legacy-remnant investigation — Gray Crow, old faction members, and Root-related files become continuing threats after Danzō’s death, prompting the establishment of Shadowbreaker. 88 95 98 121 134

Notable Quotes

“In the eyes of Root, the Uchiha were not people. They were experimental materials.” 1

“I am digging out the rotting flesh you've hidden underground, piece by piece.” — Uchiha Shingetsu to Danzō 47

“Konoha is rotting. We must carry out the Purification Plan.” — Owl 63

Trivia

• Root’s first known operation in the novel is an attempt to seize a nine-year-old orphan whose disappearance was expected to cause little attention. 1
• The organization’s use of ANBU-style equipment and seals initially complicates efforts to distinguish its activities from official village operations. 1 23
• Root’s effort to turn Shingetsu into a divisive Uchiha “banner” is explicitly characterized as “killing with praise.” 29 30
• Root’s surveillance extended beyond the Uchiha clan to Konoha’s other major clans and the Sarutobi family. 62
• The final Old Mine Town raid recovered seven living child test subjects and twenty-three stolen Sharingan were ultimately returned to the Uchiha clan. 64 65