In "Episode 359 : The Night of the Tragedy", it was revealed that Itachi sought the help of Tobi to massacre the Uchiha clan. So the following questions arise out of this situation:

  • Did he know Tobi's real identity?
  • Why did he take his help to eliminate the clan (irrespective of whether his identity was known or not)?
  • Why did he help Tobi by not revealing that he was the village infiltrator as Itachi was always working for the Village?
  • Why did Tobi agree to help Itachi eliminate his own clan?

Ideally, each question here should be a separate question, but in this scenario all these are closely inter-related and thus have been posted as a single question.

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    for your last question i gues these might be the reasons: 1. The Uchiha are extremely powerful, and would have been a major hurdle to overcome in Tobi's overall plan(infinite tsukoyomi). He needed to get rid of as many of them as possible. 2. Even if the Uchiha managed the coup, they probably would have still opposed casting an infinite Tsukuyomi. Therefore, he would still need to get rid of them. – Elysium Apr 21 '14 at 7:44
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    Also Tobi was pretending to be Madara, and since Madara was betrayed by the Uchiha, he wanted revenge. – Elysium Apr 21 '14 at 7:46
  1. The things he told Sasuke during their battle suggests that he thought that Tobi was Madara.
  2. Either because eliminating the entire clan on his own was too tough a mission for him, or because he wanted to infiltrate the Akatsuki to gather information. Also, he had Tobi promise to not hurt the Hidden Leaf or Sasuke.
  3. Because that would blow his cover. He was still protecting Sasuke and the Leaf and revealing his position would make him lose all the things he could have gotten due to #2.
  4. Because, as Madara, Tobi too had a grudge against the Uchiha. Also, he could use someone like Itachi in Akatsuki.
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  • I agree to most of the answer, except for the 4th point. It was never really shown that Tobi had a grudge against the Uchiha clan. Madara could have passed his will to Tobi, but I really doubt if the grudge against the Uchiha was passed on him as well. Can you point out to some sources where Tobi was against the Uchiha or something? – SudoRahul Apr 21 '14 at 10:37
  • what grudge did Tobi have against the village? madara's cause can be understood, but what was Tobi's? – debal Apr 21 '14 at 10:39
  • @Ɍ.Ɉ Tobi was playing Madara at the time, he wanted everyone to think that he was Madara. So he played along because Madara did indeed have a grudge against the Uchiha. – Madara's Ghost Apr 21 '14 at 10:44
  • @debal see the comment above. – Madara's Ghost Apr 21 '14 at 10:44
  • @MadaraUchiha what grudge does Tobi has against the Uchiha clan? – 3.1415926535897932384626433832 Jan 20 '15 at 3:01

Tobi aka "Obito" was just doing his mission what Madara gave to him to do , Since Obito didn't really cared about their village or his clan anymore because of Rin's death, He hates everybody for not helping Rin. He chose Itachi to join the Akatsuki because he wanted to use him in case Nagato betray him to revive Madara back to life. He was going to put the Senju cell inside of Itachi to create the Rinnegan so Madara can come back for exchange of Itachi life, But Itachi was very too smart for that and that's also why Tobi help Sasuke for the same reason.

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