Danzō Shimura

was an elder of Konohagakure. As the founder and leader of Root, Danzō gained notoriety as because of his frequent unsanctioned actions and his often-suspected (but rarely proven) undermining of specific Konoha personnel. Despite his decades of suspicious deeds, Danzō only ever acted in what he believed were the village's best interests. He was appointed the after Pain's assault on the village. Prior to being inaugurated officially into this post, Danzō would flee the Five Kage Summit and died in battle at the Samurai Bridge.

Background
Born into the Shimura Clan to his shinobi father, Danzō went onto joining the Academy, where he was amongst the first few hundred of students to graduate. From his genin days, he was acquainted with Hiruzen Sarutobi, who he became rivals with in everything. Danzō once saw the First Hokage in battle, where he witnessed Hashirama's formidable Wood Release ninjutsu.

During the First Shinobi World War, Danzō, as part of the Escort Unit alongside Kagami Uchiha, Torifu Akimichi and Team Tobirama, became surrounded by Kumogakure's Kinkaku Squad. Having concluded that a member of their team had to sacrifice themselves as a decoy in order for the rest of them to escape, Danzō struggled to bring himself to volunteer. As Hiruzen proclaimed to take the role, Danzō called himself weak while a part of him was relieved. Lashing out at Hiruzen for volunteering before he could, the Second Hokage decided to be the decoy instead, while appointing Hiruzen as his successor to Danzō's shock. The team then managed to escape at the cost of Tobirama's life.

During the Third Shinobi World War, Danzō agreed to provide aid to Hanzō of Amegakure in order to receive help in claiming the title of Hokage, sending some of his forces to deal with Akatsuki, but they were all wiped out by Nagato. In the anime, it is revealed Danzō manipulated Hanzō into joining forces with him against Akatsuki, having brought him corpses of Ame shinobi claiming they were killed by Akatsuki. In truth, they were Root members disguised as Iwa shinobi that were killed during Nagato's rampage, originally being used to disrupt a peace treaty between Konohagakure and Iwagakure in his pursuit to strengthen Konohagakure. Once the two shinobi joined forces, Danzō approached Akatsuki as an Ame shinobi named, informing them that Hanzō is allowing the group to make peace negotiations, which of course was a ruse concocted by the allied shinobi. He would later betray Hanzō at some point in history.

With Hiruzen having beaten him to the title of Hokage, Danzō began planning to someday attain the title himself. Taking up the village's more clandestine operations — something that Hiruzen noted because of his own indulgence, he allowed Danzō to do — he created the Anbu subsidiary named Root, with the organisation under Danzō's direct command. Within this group, Danzō himself hand-picked various young shinobi with noticeable potential to join.

At some point in time, Danzō also had dealings with Orochimaru, who accompanied him, along with Tatsuma Aburame, to Konoha Orphanage where he strong-armed a former Anbu agent, Nonō, to infiltrate Iwagakure and confirm the intel on what the village was planning. Soon after, Danzō notices Kabuto Yakushi spying from the window and decides to recruit the boy as well. However, in time, both Kabuto and Nonō become assets too dangerous to be left alive and Danzō tricks a brainwashed Nonō into killing Kabuto. Danzō sent Orochimaru to ensure no survivors, however, he instead took Kabuto under his wing without Danzō's knowledge. At some point, Orochimaru also surgically replaced Danzō's right arm with Shin Uchiha's, infusing the limb with Hashirama Senju's DNA to modify his physical energy. Later in the anime, when Hiruzen sought to end the bloodshed from the Third Shinobi World War through a truce with the other villages, Danzō voiced his disdain, feeling that a such an act was spitting on the memory of all the Konoha shinobi who died so far. Understanding Danzō's intent, Hiruzen decided to take responsibility for the loss by stepping down as Hokage. At a meeting with the Land of Fire Council, Danzō strongly suggested that Orochimaru be made Fourth Hokage. Hiruzen, however, pointed out that Orochimaru had grown power-hungry and showed signs of sinister intent. Ultimately, Minato Namikaze was elected as Fourth Hokage unanimously, excluding Danzō who detested the idea, feeling that following Hiruzen's ideology will ultimately destroy Konoha.

In the anime -- during Kurama's attack on Konoha -- Danzō insisted that the Uchiha clan not be allowed to join in the defence of the village, fearing that someone like Madara Uchiha would take advantage of the situation and use the Nine-Tails against Konoha. Ultimately, he convinced Hiruzen to have the Uchiha purely protect the citizens and avoid the Nine-Tails. After Kurama was stopped, Danzō was one of the elders to suspect the Uchiha clan was behind the attack, and began a spying operation on them, relocating the Uchiha to the outskirts of the village. With the Fourth Hokage sacrificing himself to seal away the Nine-Tails inside his son, Hiruzen humbly resumed his role as Third Hokage, much to Danzō's disdain. After which, Danzō approached a grieving young Kakashi Hatake, noting that it was Hiruzen's orders for the children, even high-ranking ninja like Kakashi, to not help battle the Nine-Tails, ultimately preventing Kakashi from possibly saving his sensei and his wife. Convincing an emotional Kakashi that Hiruzen was not best for the future of the village, Kakashi agreed to join Danzō's Root division and spy on Hiruzen for him. Later, as the Third Hokage resumed his role, Danzō, no longer able to tolerate Hiruzen's overly-passive methods, sought to dispose of him. He sent several Root members to assassinate Hiruzen. However, a smug Danzō was soon approached by Hiruzen, who revealed that Kakashi informed him of the assassination attempt. As Danzō feared for his life knowing he would be executed for his treasonous actions, Hiruzen calmly chose to spare Danzō, keeping this event a secret on the condition Danzō agreed to dedicate his life to protecting the village. Quickly recomposing himself, Danzō plainly stated that Hiruzen's naive faith and mercy would be his end one day, to which the Third solemnly admitted may be so. Later, Danzō met with Orochimaru, telling him about the recent events and insisted they not meet for a while in fear Hiruzen might realise that Danzō and Orochimaru were behind the abduction of several Konoha citizens, to which the Sannin voiced that Hiruzen probably already has his suspicions. However, Orochimaru did another implant onto Danzō taking Shin Uchiha's Sharingan-embedded arm and placing that, alongside some of Hashirama Senju's cells, onto that of Danzō's. Later, Orochimaru's sinister actions were discovered by the Third Hokage, forcing the Sannin to abandon Konoha. When Danzō learned of this, he knew Orochimaru would most likely go to their hideout with the Iburi clan. He sent Kinoe to inform the clan of Orochimaru's arrival. Danzō's true goal was to have Kinoe capture Orochimaru, agreeing with Hiruzen that Orochimaru was too dangerous to let go rogue. Over the years, Danzō continued to recruit new members of Root, including Torune Aburame of the Aburame clan. Three years after Orochimaru's defection from the village, fearing that his stolen Sharingan eye would soon go blind from its overuse, Danzō sent Kinoe in an attempt to steal Kakashi's Sharingan as a replacement. Kinoe soon returned, having chose to abandon his mission, much to Danzō's fury. Reminding the young shinobi of his duties as a Root member, Kinoe insisted that they should not attack allies to Konoha, which Danzō proclaimed that Root's only true allies is its own and exists only to protect Konoha itself. Unable to accept Danzō's cold views, Kinoe spoke out, making his feelings known. Horrified to see how much Kinoe had changed, Danzō used his Sharingan to incapacitate Kinoe, having one of his men take Kinoe to have his cursed seal activated. As Danzō arrived at the operating room, he discovered Kakashi freeing Kinoe and retreating with him. Danzō and his men soon surrounded the duo. As Kinoe was still under Danzō's command and Kakashi had trespassed on Root territory, Danzō had full authority to execute them. Before Danzō could act, the Third Hokage arrived, revealing that Kakashi was sent on his orders with a summoning request to be delivered to Danzō. No longer able to attack, Danzō faked ignorance of Hiruzen's letter and called off his men. Hiruzen then spoke to Danzō about Kinoe and his abilities. Insisting that Konoha need the Wood Release, Danzō agreed to hand over Kinoe to Hiruzen's command but chose to not remove Kinoe's cursed seal. Three years later, a potential alliance between Konoha and the Land of Woods was made. While a team was sent to exchange secret scrolls with the Wood-nin as a sign of trust, a small team of Anbu, under Danzō's command, was sent to observe under the suspicion that the Wood-nin would betray Konoha, in which case, the Anbu were ordered to kill them. Danzō chose Kakashi, still having high respect for his abilities, and the new recruit Danzō recommended into Anbu, Itachi Uchiha, as a two-man team for the mission.

Two years later, when word reached Konoha's leadership of a planned coup d'état by the Uchiha clan, Danzō took advantage of Itachi Uchiha's pacifist tendencies and convinced him to provide him and the other elders with information of the clan's actions. When Shisui Uchiha, acknowledged for his unquestionable loyalty to Konohagakure, presented his plan of ceasing the Uchiha's coup by casting Kotoamatsukami on his clansmen to the Council, Hiruzen agreed. Danzō, however, determined to protect the village in his own way and, believing that Shisui may try to manipulate him as well, stole the latter's right eye, implanting it into his socket, with Shisui committing suicide sometime later. When Hiruzen decided to end the coup diplomatically, Danzō secretly met with Itachi and inveigled him into choosing to slaughter his clan by presenting him with the option of killing them and sparing his younger brother, Sasuke Uchiha or letting them go through with the coup, and having them all killed as a result. Itachi regretfully chose to agree to killing the Uchiha clan.

Soon after performing the deed, Danzō told everyone that Itachi had done this out of his own will, having grown to despise his clan and even sought greater power by stealing Shisui's eyes. While everyone else believed this fabricated story, Hiruzen saw through Danzō's lie, voicing his disgust at Danzō's actions. While trying to justify his actions by claiming it was for the village, Hiruzen retorted that the Uchiha were part of the village. No longer able to trust Danzō and his underhanded ways, Hiruzen immediately removed him from the Council and ordered for his Root division to be disbanded. Afterwards, Itachi, disguised as a Root member, approached Danzō and threatened to expose Konoha's secrets to the other countries if Danzō ever harmed Sasuke. He met with Tobi around this time for reasons unknown. Over the years, despite his Root division being officially disbanded, Danzō continued to keep it secretly active.

During the Konoha Crush, the Fourth Raikage insinuated that the invasion was a secret plot of Danzō with Akatsuki to dispose of both the Hiruzen and the Fourth Kazekage, however, it is unknown whether this really happened. After seeing Hiruzen sacrifice himself using the Dead Demon Consuming Seal to defeat Orochimaru, Danzō decided to teach Sai how to use a powerful fūinjutsu, in order to prevent the same from happening to himself. During the training, Danzō noted that Sai could use "emotional energy" to bolster the power of the attack, but warned the young man not to fall prey to his negative emotions.

In the anime, Danzō revealed that he had apparently been in touch with Hanzō even after his betrayal. When Hanzō suddenly stopped contacting him, Danzō met with the Konoha Council, and told them to keep an eye on the genin sent by Amegakure to the joint Chūnin Exams, suspecting that Hanzō is no longer alive.

Personality
When he was younger, Danzō was a hot-headed and eager ninja with a strong desire to prove himself. He, after a long internal struggle, decided to volunteer himself to buy time for his team-mates, though Hiruzen Sarutobi beat him to it. He often displayed jealousy towards Hiruzen, believing he was always one step ahead of him and feeling inferior to him. Danzō never used soft words like "friend", as he never wanted to lean on someone or be leaned on. As an adult, Danzō was a completely calm, cold and collected individual who did not allow his emotions to surface. Due to being raised in times of war, Danzō's beliefs differed from those of the Hokage as he felt that the interests of the village should be placed above all else, even ethics and morals. Danzō seemed to hate the previous Hokage's beliefs stating those beliefs have destroyed the village after Pain's assault on it, despite using the attack as an attempt to overthrow Tsunade and leaving its citizens in peril as well as being responsible for Nagato's negative perceptions of Konoha, which lead to its destruction. According to Koharu Utatane, Danzō was very ambitious, but she also stated that all he ever did was for the sake of the village. In the anime, his desire to be a greater and stronger Hokage than Hiruzen made him even attempt to have Hiruzen assassinated in the belief that the Third Hokage had lost the capacity to effectively lead the village. An extremist, Danzō preferred to directly eliminate threats through assassination and execution rather than diplomacy and negotiation. However, he secretly worked closely with the international criminal Orochimaru in illegal experiments in order to increase his physical capabilities. Danzō possessed a fanatical and arbitrary adherence to the ideals of a shinobi, believing they must sacrifice absolutely everything for the village. However, Danzō hypocritically feared death, hiding this fear behind a belief that his survival was necessary for the sake of the shinobi world itself. He would only conquer this fear in the last moments of his life, boldly attempting to kill Sasuke and Tobi for the sake of his village and the entire shinobi world with his suicide, and destroying Shisui's eye with his dying breath.

Despite his reputation as a militarist, Danzō ultimately sought peace for the ninja world, one he would achieve by uniting all shinobi forces under his control. As such, he sought the title of Hokage, waiting patiently for decades before an opportunity arose. Danzō's pursuit of peace followed an ends justifies the means. As such, he had no remorse taking any immoral actions as long as he believed it would benefit Konoha. To that end, he worked in the shadows to ensure that this future came to fruition. He used Root to eliminate potential threats to Konohagakure with or without the consent of the Hokage and to further him along the path to achieving the position, as he believed he was best prepared for the "necessary" transition. Because of the nature of his actions, Danzō could not allow the details of what he had done to become public knowledge, and thus he branded members of Root with cursed seals to prevent them from revealing his secrets. Danzō also believed Konoha was strongest and most stable when the village had a target to focus its anger and hatred on. To this end, Danzō was key in stigmatizing the Uchiha clan to the rest of the village and was the one to secretly leak out the knowledge that Naruto Uzumaki was the container of the Nine-Tailed Fox, ensuring the villagers would loathe him as a result. Danzō also views the members of Root as expendables pawns and shows no remorse in having them perform duties that could result in permanent injury as shown in his ordering Fū to gouge out Ao's Byakugan, despite the fact it would result in Fū losing his eye as well.

Danzō is also treacherous by nature, as shown in his betrayal of Hanzō despite their previous alliance. Likewise, should an "ally" prove too capable for his comfort, Danzō will see to their elimination, as he attempted to do with both Nonō and Kabuto Yakushi. Itachi also believed Danzō had no intention of honouring his promise of sparing Sasuke when he accepted the mission to kill his own clan and had to threaten to leak Konoha's secrets to enemy villages and risk his own safety by returning to Konoha after Hiruzen's death to ensure Sasuke's safety. He was willing to do anything to further his physical and political powers, as shown in allowing himself to be experimented on with Hashirama's cells by Orochimaru in order to gain the power to control a tailed beast and extend his use of Izanagi. He also broke international law by manipulating Mifune into making him supreme commander of the Allied Shinobi Forces. In his later years, Danzō had become somewhat delusional, believing that he would be able to change the Shinobi World, even though his actions at the Kage Summit lost him his credibility. Danzō also had no hesitation in stealing Shisui's right eye in order to gain access to Kotoamatsukami despite his unquestionable loyalty to Konoha over his own clan and the fact he was a descendant of someone who had once been Danzō's own comrade. Tobi deduced Danzō's intent to seize control of the Nine-Tails from Naruto by using his multiple Sharingan. Danzō is also shown to be extremely arrogant, as seen in his gloating during his final clash with Sasuke, believing he had won, and only he is capable of changing the entire world.

Despite his self-righteous, amoral, and draconian methods, Danzō had a sense of nobility and dignity. He reprimanded Sasuke for his hatred and violence against Konoha, saying that it had wasted both the sacrifice of the Uchiha and Itachi's own personal sacrifices. Like Hiruzen, he used the final moments of his life to help Konoha by trying to take Sasuke and Tobi with him. Despite his envy against the Third and their growing rivalry, he seemed to still care for his boyhood friendship with Hiruzen, reminiscing of his childhood memories with him and asking what he was to Hiruzen in his final moments. His fellow elders, Homura Mitokado and Koharu Utatane, held Danzō in high regard, and often took his advice when dealing with the politics of the village. It is unknown how much they knew about the full extent of his actions.

Appearance
Danzō appeared as a frail, old man, who would normally walk with a cane. He had black, shaggy hair, and his right eye was bandaged — concealing a Sharingan underneath. Danzō has had an x-shaped scar on his chin ever since his youth. He wore a white shirt, with a black or dark grey robe over the top of it covering from his feet, to just over his right shoulder. The robe conceals his right arm which was bandaged, and covered with three large golden braces. The bandages hid an arm implanted with ten more Sharingan, originally belonging to Shin Uchiha, and the image of the First Hokage's face protruding from his right shoulder where Hashirama's cells were injected into his body.

In his youth Danzō was quite handsome. He had the same shaggy hairstyle, except it was much longer, reaching eye level. He also wore the standard armour of that era, which covered his back, chest areas and lower abdomen while leaving his shoulders armourless. With this he wore a black outfit with matching wrist guards, a shuriken holster on his right upper leg, a pouch tied to his waist with bandages, and a forehead protector. At that time, he still has both of his normal brown eyes. He hid the right eye with bandages by the time he united with Hanzō in their attack against Akatsuki led by Yahiko, and wore a flak jacket. It was also shown that at least around the time of the Third Shinobi World War, he wore a black, hooded trench coat and high-length sandals. As a child, Danzō's attire consisted of a short dark-green kimono tied with a sash.

Abilities
As the leader of the Root and the Sixth Hokage Candidate, Danzō was likely a formidable shinobi. Danzō's skills were held in high regard by the elders Homura and Koharu as they considered him one of Konoha's strongest ninja, even up until his death. His power was such that Kakashi expressed intense shock learning that he had been defeated single-handedly by Sasuke Uchiha. However, this defeat was partly attributed to his old age and because he was holding back to fight Tobi and unable to use Shisui Uchiha's Mangekyō Sharingan.

Body Modifications
Danzō's right eye was that of Shisui Uchiha's Sharingan. In the anime, Shisui's was not the first Sharingan Danzō had. He was very skilled at using it, able to detect multiple assassins in an area. He could also use Kotoamatsukami: the ultimate genjutsu of Shisui's Mangekyō Sharingan, through which he could manipulate other people's thoughts without them being aware of it. This technique seemingly did not require direct eye contact, as demonstrated when Danzō manipulated Mifune's thoughts without exposing his Sharingan. Danzō stated that it was not an ability he could use frequently. Danzō has even stated that Orochimaru's data could help with his eye; presumably wanting to increase his ability to use it. Just before his death, Danzō destroyed the eye in fear that it could one day be used against Konoha.

Danzō's most fearsome trait was his right arm: originally belonging to Shin Uchiha, Danzō's arm was implanted with ten Sharingan and was enhanced with Hashirama Senju's DNA. Ao also noted that the colour of the chakra in his right arm was also that of Shisui's. He normally kept the arm hidden under bandages and a gauntlet-like seal, presumably to conserve chakra and keep the eyes and DNA in check. Although he could not see through the eyes or use their passive abilities, he was able to perform Izanagi, a technique forbidden even amongst the Uchiha clan. When activated, Danzō temporarily gained the power to turn his own body into a physical illusion, which could nullify any injury he received from an opponent. This allowed him to survive otherwise fatal attacks while retaining the ability to inflict physical harm to his opponent. Izanagi gave him another benefit; after being "killed", Danzō would appear elsewhere away from danger. Using this technique, Danzō was able to catch Shisui off guard and steal his Sharingan.

However, the side effect of the technique was that for every 60 seconds Izanagi remained activated, Danzō would lose the use of one of his Sharingan. Also, even with Danzō's physical energy augmented by Hashirama's cells, it still took a substantial amount of chakra to sustain the technique. Danzō was implied to be able to use Shisui's eye for Izanagi, but did not in order to avoid sacrificing Kotoamatsukami. Danzō's Izanagi is considered incomplete, due to his lack of mastery over Hashirama's cells. Regardless, Danzō would abuse the usage of Izanagi to keep himself invincible for a maximum of ten minutes when he felt it was necessary, as opposed to the original meaning of the technique to be a last resort for the wielder to change a situation to their favour.

Due to integration of Hashirama's cells, Danzō also gained the shinobi's ability to heal nearly any wound without the use of hand seals. According to Tobi, Danzō's possession of both Uchiha and Senju DNA, most likely meant that he was after Naruto, with the potential capability to control Kurama.

Nature Transformation
Danzō could utilise multiple nature transformations which included Wind, Earth, Water, and Fire Release, as well as Yin and Yang Release. He was particularly proficient in Wind Release, exhaling powerful vacuum-based attacks that could either slash like blades or pierce like bullets. If needed, he could use enhanced or localised variations, some of which were strong enough to destroy an extremely durable wooden dome or damage a humanoid Susanoo's defences. Danzo could also use his wind chakra to manoeuvre himself in mid-air, as well as infuse wind into his weapons to increase their offensive power.

Possessing the First Hokage's cells in his right arm granted Danzō the ability to use Wood Release, albeit with a significant toll on his chakra. This combined, with the fact that his overall skill with this technique was quite rudimentary, prompted him to only use it when necessary. It also appeared that he could only use the Wood Release from his right, augmented arm, although he could do so without using hand seals. However, after suffering a fatal wound in his battle against Sasuke, Danzō lost control of Hashirama's cells, which began to rapidly grow into a large tree that threatened to engulf him completely. To prevent that, he broke off his right arm, causing him to lose this ability.

Fūinjutsu
Danzō was well-versed in fūinjutsu and cursed seals. To prevent his secrets from being exposed, Danzō placed binding seals on the tongues of every Root member. Should a Root member speak openly of Root and Danzō's activities, the seal would activate and instantly paralyse the member's body. The seals vanished when Danzō died. Danzō could also implement binding seals in battle, which was shown when he placed the seal on Sasuke, temporarily paralysing him. Lastly, upon his death, Danzō revealed his most powerful sealing technique, the Reverse Four Symbols Sealing. The technique caused four seal symbols on Danzō's skin to exit from his body and forms a large sphere around him. Everything inside the sphere was then drawn in and imprisoned within his corpse. After the sealing was complete, the seals could still be seen on Danzō's body.

Summoning Technique
Danzō had access to a very unique summoning, a giant tapir-like creature known as a Baku, described as the "Nightmare-Eater". A creature of massive size, it had the ability to suck in objects and targets within the area in front of it. The Baku's suction could also be used to increase the power of Danzō's wind techniques. However, using the suction left the creature vulnerable against fire techniques.

Other Skills
Danzō was adept in both using and dispelling high-level genjutsu, even from powerful Sharingan-users like Sasuke. He also had some skill in taijutsu and a decent amount of physical strength despite his old age, being able to repel Karin with one kick. Danzō was also quite fast and agile as he was able to catch Sasuke off-guard and, in the anime, was able to evade a large amount of debris falling on him. Additionally Danzō was also skilled in the use of kenjutsu, as seen against the Prajñā Group.

Tenchi Bridge Reconnaissance Mission
Danzō assigned Sai to Team Kakashi as part of a plan to secretly assassinate Sasuke Uchiha. To achieve that goal, Danzō had Sai make contact with Orochimaru in a ruse to make it seem he wanted to join forces with him to destroy Konoha. When Sai failed his mission but asked to remain with Team Kakashi, Danzō allowed him to do so while reminding the young man that emotions brought hatred, which in turn led to war.

Twelve Guardian Ninja
In the anime, Danzō was shown being followed by Anbu agents, on Tsunade's orders, when he was to be briefed by Tatsuji — a spy of his in Amegakure. He and Tatsuji were apprehended by the Anbu and later questioned by Tsunade, although the interrogation was interrupted by Sora, who was discovered eavesdropping.

Pain's Assault
When Pain began his assault on Konoha, Tsunade asked the toad Kōsuke to retrieve Naruto Uzumaki from Mount Myōboku to help defend the village. In the anime, Danzō went to Homura and Koharu to tell them that Tsunade was risking the possible loss of the Fourth Hokage's legacy and the Nine-Tails by calling Naruto back. In the manga however, Danzō waited until everyone had left the room and killed Kōsuke in an attempt to stop Naruto from returning, Danzō then gathered his Root Anbu and instructed them not to aid Konoha in the hopes that Pain's actions would end Tsunade's reign as Hokage. When asked if all the villagers would not then die, Danzō denied this, claiming that Tsunade's medical abilities would save most of them.

Following the invasion, leaders of the Land of Fire and Konoha gathered for an emergency meeting. Here, despite Shikaku Nara's best efforts, Danzō convinced the daimyō that previous Hokage's peaceful ideologies had made Konoha weak and presented himself as the type of leader the village currently needed to enforce the laws of shinobi and bring order to the world. After brief consideration, the daimyō agreed to appoint him as Sixth Hokage Candidate.

Five Kage Summit
When Danzō returned from the meeting he received a letter from the Fourth Raikage, informing him of the approaching Kage Summit and the actions of Sasuke Uchiha. As his first order, Danzō ordered Sasuke's execution for treason marking him as a missing-nin. Although he would have preferred confining Naruto to protect the Nine-Tails, Danzō was aware of Naruto's new-found popularity in the village following his defeat of Pain and settled to have Naruto watched by his agents at all times to ensure he could be made an official Hokage. He also delayed Anko Mitarashi's assassination while ordering his men to find Kabuto Yakushi instead, who was in possession of medical information that could help with his right eye and arm. Danzō later departed for the Kage Summit with Torune Aburame and Fū Yamanaka as his bodyguards, revealing the Sharingan in his right eye socket when they were ambushed by remnant shinobi of the Land of Woods along the way.

Upon arrival in the Land of Iron and the meeting's start, Danzō did not actively participate other than reporting to the other Kage of "Madara Uchiha"'s involvement with Akatsuki. Mifune suggested that the five Kage form an alliance of their villages to eliminate Akatsuki with Danzō as its leader. As the Fourth Raikage accuses him and Akatsuki, rather than Orochimaru, of staging the Konoha Crush to dispose of Hiruzen and the Fourth Kazekage, Ao exposes Danzō's manipulating Mifune before White Zetsu appeared and revealed that Sasuke was nearby. As the Raikage left to eliminate Sasuke, with Ao instructed to keep an eye on Danzō, who explained to the remaining Kage that his ultimate goal was to unify the shinobi nations under one empire, ending the possibility of future war between them.

When Sasuke arrived at their location, Danzō and his bodyguards used the opportunity to flee, with Ao in close pursuit. At some point during their escape, Danzō's party was beset by Black Zetsu's Spore Technique, but managed to dispatch the clones. Danzō ordered Fū to stop Ao, and emphasised that the retrieval of his Byakugan was a top priority. Fū managed to throw Ao off their trail, but failed to retrieve the Byakugan.

On their way back to Konoha, Danzō and his men were confronted by Tobi at the Samurai Bridge. Danzō instructed Fū and Torune to distract Tobi while he unsealed his right arm. Once Fū and Torune were defeated, Tobi brought out Sasuke. Danzō, revealed his right arm to show that it was embedded with Sharingan all over, and voiced his intent to add Tobi's and Sasuke's to his collection. Sasuke immediately questioned him about the Uchiha clan's assassination, hoping to find out if the Konoha elders really did force Itachi to murder his family. Danzō confirmed the story and questioned why Itachi would sacrifice peace to tell Sasuke the truth. Angry that Danzō spoke about his brother so casually, Sasuke crushed him with his Susanoo's hand.

Despite his apparent death, Danzō was unharmed by Susanoo, as well as Sasuke's subsequent attacks. All the while Danzō goaded Sasuke by constantly talking about Itachi, prompting him to fully develop his Susanoo. Sasuke used Susanoo to fire an arrow at Danzō, who was forced to use his Wood Release to divert the attack. Tobi, having been observing the battle, surmised that his use of Sharingan and Wood Release must mean that he planned to control the Nine-Tails as well, and that he was using Izanagi, with the many Sharingan on his arm being sacrificed one-by-one to escape death. When he was finally reduced to one, Danzō and Sasuke each prepared one final attack; breathing wind-natured chakra onto a kunai creating a blade, Danzō prepared to clash with Sasuke's Chidori Sharp Spear.

Danzō believed that he had won and told Sasuke to go and join Itachi, before realising that Sasuke's genjutsu tricked him into thinking he has one more eye left to evade the impalement. His depleted chakra levels, coupled with his new injury, caused him to lose control of his wood abilities and he was forced to sever his arm before he was turned into a giant tree. Refusing to accept defeat, Danzō takes Karin as a hostage and prepared to use Shisui's eye before Sasuke extended a Chidori Sharp Spear through Karin to stab Danzō's heart.

Dying, Danzō staggered towards Sasuke and Tobi, thinking about Hiruzen and how, no matter what he did, he could never match him, not even having properly become Hokage. With his last breath, he proclaimed that for the sake of the world and the safety of Konoha, he would take Sasuke and Tobi with him to the grave. He then activated the Reverse Four Symbols Sealing, but Sasuke and Tobi were able to get out of range. Danzō was, nevertheless, able to destroy Shisui's Sharingan in order to prevent Tobi from obtaining it.

Legacy
Danzō is widely recognised as being one of the leading figures in the village's growth after the death of the Second Hokage. Acting as Hiruzen's top intelligence advisor and through his own sanctioned actions, Danzō's willingness to take on the dark, but vital tasks of the village such as management of espionage and assassinations of high profile threats were crucial to the success of the village. Though the true extent to which Danzō has both influenced and protected the ninja world will remain predominantly unknown, certain people — especially those in Root — remain adamant that if it were not for Danzō and his actions, peace would not have been maintained for so long. He made it a point to eradicate any opposition to Konoha that would destroy the peace that the village enjoyed. As his final act in protecting the village, he attempted to kill Sasuke Uchiha, a missing-nin from the village, as well as Tobi, the mastermind of the terrorist organisation Akatsuki. Unsuccessful in this, however, in order to thwart Tobi's plans, Danzō crushed Shisui Uchiha's Sharingan before dying. Though he has done a great deal in the way of protecting Konoha, Danzō had a manipulative, duplicitous and militant perspective born from the era of the Three Great Wars, and at times, he was unable to fully clean up and control the blowback of some operations, such as in the case of Nagato, Kabuto and Sasuke. Despite this, the actions of Danzō, Homura, Koharu and Sarutobi regarding the Uchiha clan did avoid a world scale conflict, which Sarutobi had failed to stop diplomatically. In an ironic turn of events, Sasuke had later unwittingly taken up many of Danzō's traits during the Fourth Shinobi World War after deciding to protect the village, proclaiming that he would change the system of shinobi that he considers the source of all the chaos the ninja world has endured. After the war, though he remains acting mostly in the shadows, he is not as ruthless as Danzō.

After Danzō's demise, Kakashi and Tsunade worked to tie up all loose ends, researching remaining Root facilities and members. However, not wanting the ex-Root members to become ostracised because of their history with him, the two Hokage chose not to publicly announce their final report. Also, one of Danzō's most loyal followers and top researchers, Tanuki Shigaraki grew to resent the village for Danzō's death and by extension the disbanding of Root. Wanting revenge, he worked to complete his final project entrusted to him by Danzō, the Gozu Tennō, as a means for his goal.

Trivia

 * Elements of Danzō's design and backstory, including the x-shaped scar on his chin and his status as the leader of Root, appear to have been taken from Kishimoto's original concept for Itachi Uchiha, as revealed in Naruto Hiden: Jin no Sho Character Official Data Book.
 * Like Dan Katō, Danzō's name may be a reference to Katō Danzō, a noted ninja master during the time of the Sengoku period of Japan.
 * Danzō's family name, Shimura, is written with the kanji for and  and can be interpreted as "I did it for the village," possibly hinting at Danzō's true intentions.
 * Danzō's relationship with Hiruzen Sarutobi was very much like Naruto's rivalry with Sasuke, where Danzō felt that Hiruzen was always "one step ahead of him" in every way.
 * Although a well-intentioned extremist, Danzō's actions have ironically enough made him a primary catalyst for the formation of the villainous world views of both Nagato and Kabuto Yakushi, as evidenced by their flashbacks. This also made him the reason for many of the protagonists' troubles throughout much of the story, most particular is the eventual rise of Sasuke's bitter and merciless vendetta against Konohagakure.
 * Danzō's death is similar to Deidara's, as both involve last ditch efforts against Sasuke Uchiha.
 * Studio Pierrot's Settei sheets of Danzō show that he was 146cm around the time the Valley of the End was created, and 168cm when Tobirama died.
 * In the fourth databook, summoning is not listed among Danzō's special characteristics. Also, despite his usage of Izanagi, a technique based on the Six Paths' Creation of All Things Technique, Yang Release wasn't listed as one of his natures.
 * According to the databook(s):
 * Danzō's hobbies were appreciating famous pictures, and keeping diaries.
 * Danzō's favourite food and drink was hijiki (which he shared with his rival Hiruzen Sarutobi) and genmaicha (brown rice tea), while his least favourite was warabimochi (jelly-like confection).
 * Danzō did not want to fight anyone in particular.
 * Danzō's favourite word was.

Quotes

 * (To Hiruzen) "My father and grandfather died in battle as ninja. Self-sacrifice is a ninja's duty."
 * (To Kinoe) "The world of the shinobi is filled with a myriad of techniques. You cannot compete with just one power. We must master various techniques and use those powers to unite the shinobi world."
 * (To Sai) "Emotions lead one to hate… and hate leads one to conflict and war…"
 * (Danzō on not being well known in the ninja world) "The ninja world is an ascetic world. To remain anonymous is a source of pride. But by controlling both the surface and underground, one can truly strengthen the village and nation. I will make certain that this summit is a success and that I am recognised as Hokage. Then the jōnin will have no choice but to accept me as Hokage. My era has finally come."
 * (To Sasuke) "Self sacrifice, that's what epitomises a shinobi. Never seeing the light of day, toiling in the shadows. That's the way of a true shinobi and not just Itachi. Countless shinobi have died the same way. This world could not function on ideals and pleasantries. It's thanks to people like him that peace has been maintained."
 * (To Sasuke) "Two brothers, whose abilities are identical. How could what your eyes perceive be so different. The truth about Itachi isn't important to you at all. Instead you simply want to destroy everything with your hatred. All you're doing is making the sacrifice of the Uchiha clan meaningless."
 * (To Sasuke) "It's not my life I'm worried about. This is for Konoha… for the ninja world… I can't die now… I'll… do anything… to survive. I… am the only one… who can change this world… this girl will be sacrificed for that."
 * (Last words) "Hiruzen… it looks like it's my turn next… but I… never did become Hokage… no matter how far I went I could never catch up with you… you are the leaves bathing in the sun. I… am the roots that grow in the dark. Hey, Hiruzen… what do you think of me? What am I to you…?"