Uchiha Clan Downfall

The, also called the , was the massacre of the Uchiha clan by Itachi Uchiha and — unbeknownst to most — a man claiming to be Madara Uchiha.

Background
Following the Nine-Tailed Demon Fox's Attack, Konohagakure's leadership began to suspect that the Uchiha were behind the attack due to the Sharingan's ability to control the beast. From that point onwards, the Uchiha were placed under close surveillance — something Tobi claims was accomplished by forcing all Uchiha to live in one section of the village. This mistrust and isolation from the rest of the village created feelings of ill-will amongst the Uchiha, and ultimately rekindled the hatred harboured towards the Senju-influenced government. As such, the Uchiha — led by Fugaku Uchiha — began planning a coup d'état to overthrow the Konoha leadership.

In preparation for the coup, the Uchiha started inserting its members within Konoha's command structure to act as spies. Itachi was placed in the Anbu, the direct arm of the Hokage. However, Itachi did not agree with the Uchiha's plans, believing the coup would only escalate into another Shinobi World War. As such, he turned double-agent, providing Konoha with information on the Uchiha's plans. The Third Hokage, who did not agree with the treatment of the Uchiha following the Nine-Tailed Fox incident, tried to find a peaceful resolution with the clan. Danzō Shimura, however, did not believe negotiations would solve anything and felt eliminating all the Uchiha would cause the least bloodshed.

The Uchiha noticed Itachi's strange behaviour and tasked Shisui Uchiha with keeping an eye on him. Shisui, a close friend of Itachi, shared his opposition to the coup. When peace talks started to break down, Shisui attempted to use his Mangekyō Sharingan's Kotoamatsukami to force the Uchiha's leaders to change their minds. Danzō felt this was a waste of Kotoamatsukami's rare usage, as it could only be used once every ten years, and took Shisui's right eye for himself before Shisui had a chance to use it. Having failed and fearful that Danzō would take his other eye, too, Shisui entrusted his left eye to Itachi before committing suicide. After finding his body, the Uchiha believed Shisui, whom they had sent to spy on Itachi, had been murdered by Itachi and that he had staged Shisui's suicide and, as such, no longer trusted him.

Although he still wanted to find a non-violent solution, Shisui's death convinced Itachi that events could no longer be stopped. He became outwardly critical of the clan's actions and hostile towards individual members. Danzō, aware of Itachi's conflicted feelings, explained the two possible outcomes: the Uchiha could be allowed to attempt their coup, an act that would ultimately lead to the entire clan's extermination, including Itachi and his younger brother, Sasuke Uchiha; alternatively, Itachi could assassinate all the Uchiha before the coup took place, and in exchange would be allowed to spare Sasuke's life. Itachi opted to save his brother.

Before carrying out the massacre, Itachi found Tobi sneaking around the village. Believing he was the real Madara Uchiha bent on destroying Konoha, Itachi offered to help him take revenge against the Uchiha for betraying him decades earlier if he would spare the village, which Tobi agreed to. Tobi, under the guise of Madara, also met with Danzō around the same time for unknown purposes.

Attack
In a single night, Itachi and Tobi slaughtered the entire Uchiha clan. In the anime, Tobi slaughtered the military portion of the Uchiha Clan by directly attacking the Konoha Military Police Force headquarters, enabling Itachi to slaughter the civilian portion without much resistance, and Tobi also secretly took some of the Uchiha's corpses for himself. Itachi expected Fugaku to be the greatest enemy and entered his home with great caution. To his complete surprise, both his parents were willing to accept death rather than fight their son. Both respected his decision to side with the village over the clan, and asked only that he look after Sasuke. He tearfully killed them just before Sasuke returned home from the Academy.

Although he knew his actions were necessary, Itachi could not forgive himself for killing his own family and believed he had to be punished. Sasuke, a child and thus ignorant of the Uchiha's conspiracies, was the only person qualified to pass the judgement on Itachi he felt he deserved. As such, Itachi attacked Sasuke when he entered their house, desperate to make Sasuke believe he had killed their clan without provocation and for selfish pursuits of power. He used Tsukuyomi to torment Sasuke with images of the clan's murder and claimed Sasuke was too weak to even bother killing. Itachi encouraged Sasuke to embrace hatred and vengeance in order to get stronger and to come after and kill him to avenge their family.

As Itachi left, Sasuke made an immediate attempt to follow Itachi's instructions; awakening his Sharingan for the first time, Sasuke pursued Itachi and attacked him, managing to knock off his forehead protector. Itachi wept from Sasuke's action, but continued on after collecting his forehead protector. Sasuke passed out from the traumas of the night and would not remember this moment of retaliation for many years.

Aftermath
Only three Uchiha survived the clan's massacre: Itachi, Sasuke, and Tobi, though most of the world, Sasuke included, did not know of Tobi's involvement in the massacre or survival.

Itachi reported the mission's success to the Third Hokage. The Third, having been unaware of Itachi's assignment from Danzō, regretted to hear the news. With nothing to be done about it now, the Third promised to perpetuate the cover story that Itachi had acted alone and without cause so that nobody would learn of the Uchiha's plans, and also so that Konoha would not be tarnished for its involvement. Most important to Itachi, the Third vowed to keep Sasuke safe from Danzō. In the anime, the Third also ordered the dissolution of Danzō's Root and his removal from the council as punishment for acting without his permission. Itachi then left the village, joining the organisation Akatsuki, in order to reinforce his image as a criminal. In actuality, he monitored Akatsuki from the inside, keeping Konoha informed of its actions and preventing the organisation from moving against the village. Itachi also threatened to reveal all of Konoha's confidential information to foreign forces should Danzō bring harm to Sasuke.

True to Itachi's intentions, the Uchiha's massacre had an immense impact on Sasuke. Sasuke's sole motivation over the following years was to become strong enough to kill Itachi, first by training as a shinobi of Konoha and later, after being dissatisfied by his slow growth in Konoha, by defecting to Orochimaru. Under Orochimaru, Sasuke gained enough power to finally pose a threat to Itachi, culminating in Itachi's death when they finally met in battle. Sasuke enjoyed a brief moment of believing he had avenged his family at last, but was shortly afterwards approached by Tobi and informed of the truth behind Itachi's actions. After realising that Itachi only ever acted in the interests of his village, Sasuke decided to destroy Konoha for what they did to his brother. However, after reconciling with a reincarnated Itachi and Hashirama, Sasuke decided that this would be contradictory to what Itachi sacrificed his life for and that he would instead protect the village.

The truth behind the massacre was successfully kept a secret for many years, though Kabuto Yakushi — an experienced spy — was able to uncover it at some point. After Itachi's death, however, Tobi no longer felt obligated to keep up the cover story and shared the truth when he deemed it convenient; he first revealed the truth to Sasuke in order to win his cooperation, and later to Naruto Uzumaki, Kakashi Hatake, and Yamato in order to defend Sasuke's actions. Furthermore, Sasuke's former Taka team-mates, and Orochimaru, were also made aware of the truth, and during the Fourth Shinobi World War, Killer B and a reincarnated Nagato also learned the truth when Naruto asked the reincarnated Itachi about it. Years later, Sakura Haruno and Sarada Uchiha learned the complete truth from Sasuke himself. Upon his reincarnation and learning that the truth had been revealed, Itachi insisted that those who knew did not publicise it so that the Uchiha clan could retain some honour.

At some point following the Fourth Shinobi World War, Naruto revealed to the world that Itachi was responsible behind the reincarnated shinobi to have been returned to the afterlife during the war, therefore ultimately assisting the Allied Shinobi Forces in emerging victorious in the war, although Naruto continued to keep Itachi's true mission and goals of the massacre a secret to honour his promise to Itachi.

Trivia

 * In the manga, Tobi stated Fugaku organised and planned the coup d'état. In the anime, however, it was stated that he did not plan it, but as the head of the Uchiha clan, he had no choice but to go along with their decision. However, he opted for an option that would satisfy the Uchiha Clan and lead to the least bloodshed. To this end, he asked Itachi to help him take over the seat of Hokage by force as well as kept his Mangekyō Sharingan hidden.
 * In the anime, it is shown that an unknown Anbu was also aware of the coup d'état. This was an error in the adaptation because at the time of the incident, only six people were aware of the truth – Tobi, Itachi, Hiruzen, Danzō, Koharu, and Homura.
 * Furthermore, in a flashback-focused episode, it's shown that Kakashi, Tenzō, and the rest of Team Ro, were told only minor details of the Uchiha's coup d'état, as they were merely told about a possible civil war, but without receiving the full details, which contradicts the statement that the Uchiha's growing resentment and mistrust towards Konoha was only known by the elders, Tobi, and Itachi.