Root

Known also as the Foundation, Root started life as a training offshoot of Konohagakure's Anbu. Danzō Shimura created it and ran it, using it to execute any operation he considered good for the village. Its core doctrine, dubbed the Will of Root, framed its agents as the hidden hands that propped up Konoha's great tree from far below the soil. That creed excused a range of ugly deeds, among them the murder of people marked as possible threats simply for speaking ill of the village, even when they had committed no actual offense against it. Above everything the group prized secrecy, and the bulk of its work played out in shadow, beholden to no link in Konoha's command chain and shielding its confidences even more jealously than the ordinary Anbu. Root was officially wound down after the Uchiha Clan Downfall, a catastrophe Danzō himself masterminded, though it carried on in secret until he died. Even once Hiruzen ordered it shut, its members held to Danzō, placing his word above the Hokage's. With Danzō gone, Sai advised the survivors to turn to Kakashi Hatake, who stood next in line for the office of Hokage.

Root forged its operatives through savage methods. A cursed seal was stamped onto the underside of each member's tongue, and the instant one tried to divulge anything concerning Danzō or the group, that seal froze the whole body rigid, guaranteeing that capture and interrogation could pry loose no secrets. The mark faded away the moment Danzō died. To burn emotion out of them, Danzō raised his recruits side by side as brothers from boyhood and then made them slaughter one another, a regimen almost indistinguishable from the old graduation trial at Kirigakure's Academy. Members answered to codenames, and plenty of them no longer recalled the names they had been born with. Rather than a katana they bore a tip-less tantō, and under the usual Anbu cloak and mask, which carried no uniform beyond a short midriff jacket in black, fitted with red straps across the shoulders, each dressed in clothing of their own. The group also leaned on gradual, drawn-out brainwashing, once slowly reworking a run of photographs so that Nonō Yakushi would no longer know Kabuto and would move against him.

The organisation's ledger of missions runs long and murky. Danzō set Tanuki Shigaraki to fashioning the Gozu Tennō weapon out of cells taken from Hashirama, sent Nonō into Iwagakure, and slipped Kabuto among the great villages to spy before plotting to make the two agents kill each other. Other jobs included framing Iwagakure to wreck peace talks, steering Hanzō into an alliance, and ordering Sai to assassinate Sasuke Uchiha, an assignment Sai in the end walked away from. While Pain laid waste to the village, Danzō held Root back from its defense, gambling that the calamity would clear his road to the office of Hokage. Setting out for the Kage Summit, he brought Fū and Torune along as guards while other agents shadowed Anko and Kabuto, but Tobi spirited the bodyguards away and Sasuke ran Danzō through before any of these plots could bear fruit.

Danzō Shimura both founded and commanded Root, handpicking its members and leaning toward recruits from clans with rare gifts, the Aburame, Yamanaka, and Uchiha among them. Sai grew into its most familiar face, ultimately defying Danzō's orders and later striving to free the remaining members from that legacy. In the anime, Yamato was the single member Danzō trained with his own hands. Nonō Yakushi, valued for her skill at gathering intelligence, was deemed unfit because she could never shed her feelings, and she met her end at Kabuto's hands. Kabuto Yakushi spied on Root's behalf before defecting alongside Orochimaru. Fū and Torune stood as the top pair and served as Danzō's guards, while Tanuki Shigaraki pressed on with the Gozu Tennō project after his exile, handing his grudge down to his daughter Sumire. Once the Fourth Shinobi World War had ended, Tsunade together with Kakashi held back the villagers' background checks, letting former agents like Kido Tsumiki and Magire slip quietly back into the regular Anbu.