Root

Biodata

Feature	Value
Name	Root (根部)
Affiliation	Konohagakure (formerly; purged following Danzō's arrest) 5 7 119 121
Occupation/Role	Former secret Konoha organization that conducted investigations, tracking operations, covert eliminations, and clandestine political operations 7 9 15
Status	Purged and being dismantled; Danzō was arrested, while Root's remaining loyalists and network were placed under investigation 119 121
First Appearance	Chapter 2

Background

Root operated beneath Konoha under Danzō's command. Its members wore masks and carried no identifying marks; they were trained to execute orders without questioning their purpose. 9

The organization had access to extensive surveillance records on Uchiha Lieyang, including his friends, businesses, public statements, mission habits, and private meetings with members of the Uchiha Police Force. Danzō regarded Lieyang's network of relationships as evidence that he was building independent influence within the village. 7

Root's surveillance and intelligence gathering failed to uncover the full extent of Lieyang's capabilities. After its personnel were killed, a Yamanaka ninja extracted fragmented memories from the dead and confirmed that Lieyang possessed unrecorded Water, Earth, and Lightning Releases, one-handed seals, Lightning Body Flicker, and independently combat-capable Shadow Clones. 14

Following the catastrophic failure of the pursuit operations, Root became a focal point of Konoha's internal political crisis. The ninja-clan and civilian shinobi factions temporarily united to demand restrictions on Danzō and a purge of Root. 65

Although Hiruzen Sarutobi initially restricted Root by reclaiming several of its mission channels for Hokage-controlled ANBU, Danzō continued using his remaining contacts, loyalists, and external political connections. He covertly supplied intelligence to Land of Fire nobles, enabled the Mikawa Family's attempt to test Lieyang, and employed operatives using Root's methods to provoke further conflict. 99 117 119 121

After Danzō's attempt to resist arrest failed, Konoha began investigating and purging Root's surviving network. The organization was dismantled as part of the effort to prevent its remnants from provoking Lieyang and endangering the village. 119 121

Organization and Methods

• Root operated from an underground base beneath Konoha. 9
• Members concealed their identities with masks and unmarked clothing. 5 9
• It deployed organized squads with jōnin captains and elite operatives. 9 12
• Its missions employed coordinated ambushes, underground Earth Style attacks, ninja-tool barrages, close-combat traps, and battlefield investigation. 9 11 12
• Root commonly used baiting tactics in which one operative deliberately exposed an opening while allies prepared the killing blow. 11
• Root gathered and preserved evidence, including sealing recovered material for later confirmation. 5
• Its agents could use summoning scrolls and messenger beasts to transmit battlefield intelligence to headquarters. 12
• Root used Konoha's Yamanaka personnel to inspect the memories of dead operatives and reconstruct combat encounters. 14
• Its squads performed reconnaissance, tracking, containment, sealing, assassination, and support functions during major operations. 15 17 23
• Under Danzō's orders, Root squads were also tasked with contacting external agents, establishing secret bases, transferring supplies, and recruiting usable assets within the Land of Fire. 15
• Root monitored the Uchiha Clan Compound and infiltrated the Konoha Police Force as part of Konoha's long-standing surveillance of the clan. 37
• Root maintained covert political and operational connections beyond its formal command structure, allowing Danzō to influence Land of Fire nobles, peripheral shinobi, and mission-related activities even after his authority had been restricted. 118 119
• Danzō's remaining network was vulnerable to Hokage intervention after Root's mission channels were revoked and its personnel suffered extensive losses during the pursuit of Lieyang. 99 119 121

Story Role / Major Arcs

Investigation of the A-Rank Mission Failure

After a forest fire destroyed the site of Takeno Sota, Ayakawa Yukina, and Uchiha Lieyang's mission, Root joined ANBU in examining the scene. Its investigators found evidence of Earth Style and Parasitic Destruction Bugs, then prioritized locating Lieyang despite all three shinobi being missing. 5

Danzō argued that Lieyang's disappearance, Fire Style traces, and the loss of his teammates were sufficient grounds to treat him as a defector. Hiruzen Sarutobi instead demanded an investigation and instructed Root to bring Lieyang back for interrogation if possible. 6 7

Hiruzen's order granted Root access to Lieyang's past records, authority to seize his businesses, interrogate people close to him, deploy trackers throughout the Land of Fire, and act directly against him. Danzō privately intended to recover Lieyang's Sharingan and brain even if he was killed. 7

First Pursuit Squad

Danzō sent two Root squads—seven masked shinobi led by two jōnin captains—with orders to bring back Lieyang's corpse and eyes. Their intelligence described him as a Three-Tomoe Sharingan special jōnin whose abilities centered on Fire Style, Wind Style, genjutsu, throwing weapons, and Shadow Clones. 9

The squads attempted an underground ambush, followed by a coordinated barrage of hundreds of kunai. Lieyang detected their positions while blindfolded and redirected their attack with the Shuriken Shadow Clone Technique. 9 10

Root's assessment deteriorated further when Lieyang used Water Style: Hidden Mist Technique, displayed overwhelming taijutsu, and employed rapid one-handed Earth Style. The squad's captain and remaining members were killed during the battle. 10 11

Flowing Moon Squad Investigation

A later Root squad discovered the Flowing Moon Squad annihilated at a battlefield marked by Earth Release, underground movement, explosive tags, ninja-tool collisions, and intense taijutsu. The dead included Captain Flowing Moon, a jōnin skilled in close combat, assassination, and battlefield command, along with three elite members. 12

Unable to reconcile the battlefield with Lieyang's existing intelligence file, the investigating captain concluded that Lieyang had been aided by at least one elite shinobi from another village. Root headquarters received the report, and Danzō ordered the investigation to continue. 12

Escalated Pursuit and Intelligence Failure

After inspecting the memories of deceased Root operatives, a Yamanaka ninja reported that Lieyang possessed Hidden Mist Technique, Earth Flow Spears, Lightning Body Flicker, one-handed seals, and Shadow Clones capable of independently using ninjutsu, swordsmanship, and genjutsu. This evidence disproved Root's belief that another village had aided Lieyang and established that its intelligence profile had been disastrously incomplete. 14

With Hiruzen's tacit approval, Danzō opened four sealed chambers in Root's underground base and dispatched four additional elite squads. While officially tasked with retrieving Lieyang's corpse and eyes, the squads also received covert instructions to expand Root's external network across the Land of Fire. 15

Three elite Root squads were annihilated in rapid succession by Lieyang's Shadow Clones, which used Lightning Body Flicker, one-handed seals, and coordinated ninjutsu to dismantle their formations. When the losses were disclosed to Konoha's upper ranks, Hiruzen confirmed that six Root squads, three regular Konoha teams, and six jōnin had been killed during the wider pursuit. 15

Root's losses led Danzō to acknowledge that Lieyang's abilities exceeded its intelligence at every stage. Its analysis ultimately classified him as a versatile Shadow-level combatant whose Lightning Body Flicker and swordsmanship bore traits comparable to Konoha's White Fang. 16

Joint Pursuit Operations

As ordinary pursuit squads proved ineffective, Root supported Hiruzen's joint suppression force under Kakashi Hatake. The force was designed around ocular tracking, genjutsu, supreme taijutsu, and coordinated restraint techniques, while Danzō ordered two more Root squads to accompany the operation. 17 19

Root reconnaissance personnel were repeatedly eliminated before they could provide useful intelligence. A reconnaissance squad was wiped out before Kakashi's force arrived at the target area, prompting Kakashi to order the remaining Root personnel not to engage Lieyang directly. 22 23

During the first joint pursuit, Root's accompanying squads lost all contact amid the collapse of the encirclement. By the time the surviving Konoha shinobi retreated, no Root operatives had returned with them. 28

Root continued to support the later suppression mission against Lieyang, but the operation ended in another devastating defeat. Kakashi Hatake, Shisui Uchiha, and Might Guy were severely wounded, Kurenai Yuhi was captured, and Lieyang took both Kakashi's and Shisui's Mangekyō Sharingan. 60

Political Fallout

Following the final defeat, Danzō received the battle report at Root headquarters and condemned his subordinates for failing to prevent the loss of two Mangekyō Sharingan. When he attempted to meet Hiruzen, ANBU guards refused him entry on the Hokage's direct order, signaling a serious rupture between Root and the Hokage. 60

The pursuit's casualties and the exposure of Root's role provoked opposition from both the ninja-clan faction and the civilian master-disciple faction. The factions jointly demanded that Danzō be restrained, Root be purged, and the Hokage's administration explain the true purpose of the manhunt. 65

Root's authority subsequently became a subject of village-wide scrutiny, with its past surveillance, covert deployments, and role in Konoha's internal repression contributing to the broader challenge against the old leadership structure. 65 68

Decline, Unauthorized Operations, and Purge

As Konoha's attitude toward Lieyang shifted from pursuit to cautious coexistence, Hiruzen reclaimed several of Root's mission channels and placed them under the direct control of the Hokage's ANBU. The transfer of Yamato from Root to ANBU also deprived Danzō of his only successful Wood Release test subject. 98 99

Despite these restrictions, Danzō continued to use Root's remaining network to influence nobles and peripheral forces in the Land of Fire. He secretly provided advance intelligence to a noble faction, encouraged the Mikawa Family to test Lieyang, and was suspected of arranging further provocations through operatives using Root's methods. 117 118 119 121

Konoha's senior jōnin concluded that its immediate danger was no longer Lieyang, who had left the Land of Fire, but Danzō and the remnants of Root that could provoke another catastrophic conflict. Tsunade consequently accepted the need for decisive action against Danzō. 117 118

ANBU forces led by Kurenai Yuhi moved to arrest Danzō under the Lord Third's authority. After Danzō resisted, Shisui Uchiha disabled his ability to form seals and used his Sharingan to incapacitate him, allowing ANBU to seal his chakra and take him into custody. 119

Following Danzō's arrest, Tsunade and Shikaku Nara oversaw an investigation and purge of Root's loyalists and remaining network. The operation was intended to prevent Root from once again dragging Konoha into conflict with Lieyang, effectively ending Root as an independent covert power. 120 121

Relationships

• Danzō — Root's former leader; directed its investigations and elimination missions against Uchiha Lieyang, while using the pursuit as cover to expand Root's external network. After Root's collapse, he continued exploiting its remnants for unauthorized political operations until his arrest. 6 9 12 15 119 121
• Hiruzen Sarutobi — Authorized Root to investigate Lieyang, while ordering that he be captured for interrogation when possible. After the final suppression operation failed, Hiruzen refused to receive Danzō and later reclaimed Root mission channels for Hokage-controlled ANBU. 7 60 99
• ANBU — Cooperated with Root at the burned mission site, though the two groups searched separately and shared limited information. ANBU later enforced the arrest of Danzō and assisted in removing Root's remaining influence. 5 119 121
• Uchiha Lieyang — Root's primary pursuit target; Root received authority to capture or kill him and suffered repeated squad losses during the hunt. Danzō's later use of Root remnants to provoke or restrain Lieyang made preventing further conflict with him a major reason for Root's purge. 7 9 12 15 117 121
• Flowing Moon Squad — Root squad led by the jōnin Flowing Moon; wiped out during the pursuit of Lieyang. 12
• Yamanaka Clan — Its mind-reading techniques were used to extract battlefield intelligence from dead Root operatives, exposing the inaccuracies in Root's records on Lieyang. 14
• Kakashi Hatake's Joint Pursuit Force — Root provided reconnaissance and squad support for the operations led by Kakashi, though its personnel were unable to withstand Lieyang's attacks. 17 22 28
• Shisui Uchiha — Voluntarily joined Root in an attempt to ease the divide between the Uchiha Clan and Konoha's higher-ups. Danzō exploited Shisui's idealism and sought control of his Kotoamatsukami; following his recovery, Shisui helped incapacitate Danzō during the latter's arrest. 37 72 119
• Uchiha Clan — Root monitored the clan and infiltrated the Konoha Police Force, contributing to the Uchiha's distrust of Konoha's leadership. 21 37
• Konoha's Ninja Clans and Civilian Shinobi Faction — United after the pursuit disaster to demand that Root be restricted and purged; their representatives later supported action against Danzō and Root's remaining network. 65 117 118
• Tsunade — As Konoha's leading authority during the transition away from the old administration, Tsunade endorsed Danzō's arrest and the uncompromising purge of Root's surviving forces. 120 121
• Kurenai Yuhi — Following her return to Konoha, Kurenai led the ANBU unit that confronted Danzō and enforced the order for him to submit to investigation. 119
• Yamato — Root created Yamato through Hashirama Cell experimentation; Hiruzen later transferred him into ANBU, weakening Danzō's control over Root's only successful Wood Release subject. 98 99
• Land of Fire Noble Faction and Mikawa Family — Danzō used Root-linked intelligence and methods to cooperate with nobles and facilitate attempts to test or provoke Lieyang, contributing to the case for Root's final purge. 118 119 121

Trivia

• Root's initial intelligence on Lieyang omitted his Water and Earth chakra natures, Shuriken Shadow Clone Technique, exceptional taijutsu, simplified hand seals, and one-handed seal casting. 10 11 12
• Its investigators interpreted the destruction of the Flowing Moon Squad as evidence of outside assistance, rather than accepting that Lieyang could have achieved it alone. 12
• Root's later postmortem intelligence confirmed that Lieyang possessed all five basic chakra natures, Lightning Body Flicker, and Shadow Clones capable of independently killing jōnin. 14 19
• Danzō used the pursuit of Lieyang not only as an elimination operation, but also as an opportunity to establish Root bases and recruit assets outside Konoha. 15
• Root's repeated reliance on familiar coordinated traps allowed Lieyang to identify and exploit its combat patterns. 11
• Root's six-squad loss during the pursuit created a major gap in the elite force Danzō had accumulated over many years. 16
• Although Root's formal authority was repeatedly reduced, Danzō retained enough loyalists and connections to continue influencing external agents and Land of Fire political factions before his arrest. 118 119
• Root's purge was driven not only by its past abuses, but by Konoha's fear that its remaining operatives could provoke Lieyang into directing his full strength against the village. 121