Unsolved mystery of Naruto Shippuden

As stated above, I need clarifications on some points.

P.S. I didn't read manga before Pain's arc, so if anything I listed is non-canon then please forgive me.

1. When, during Graverobber arc, Naruto asked Yamato that is it possible for anyone to use all 5 changes in Chakra nature, Yamato said that it's unheard of anyone possessing all 5 and even 2 was a great feat. How did he even say it when Kakashi, right next to him, and 3rd Hokage had achieved all 5 changes. (though Kakashi knowing wind style is never specifically proved but we can assume that by references, 4 is still a great feat.....and don't consider Rennegan as it was considered myth by everyone by that time).

2. If 3rd Hokage sealed Orochimaru's hand so that he couldn't use any jutsu, how did he use it against Naruto in his tailed state on the bridge after defeating Sasori (summoning jutsu).

3. When 4th Hokage was revived, how did he still have Half Nine Tails in him even when he was revived in a different body? Even if you say people could be revived in any age or state, it doesn't proof how he got half 9 tails as Orochimaru revived him in different body while 9 tails was stored in his original one. They didn't dig him out of his grave. If you say that 4th sealed even 9 tail's soul with him, then 9 tail's wouldn't have any chakra with him as souls can't posses chakra (unless you use a jutsu...like Dan). Chakra is the property of the body.

4. If Itachi was still spying Akatsuki and reporting back, why was Tsunade still so confused about current position and work of Akatsuki? Even further, she could have asked Itachi to help out Jiraya when he was invading Hidden Rain for Akastuki leader as Itachi is a very skilled ninja and Jiraya could have easily carried him in his toad the same way he shrinks his enemy with him. Together they had high chance of dealing with and possibly beating Pain. What's the point of spying on someone when you don't supply his info. And if you say the deal was just till 3rd's time, why did Itachi come back after his death to check on Sasuke and whether the deal was followed or not; if you can't keep your end of bargain, why would others.

5. Why didn't Nagato revive Yahiko using his Rennegan when Yahiko died during the battle with Hanzo? At that time you may say that Nagato couldn't control his Rennegan but if he still carried Yahiko's body around, he could have revived him later when he had control on his 7th path of pain. If he had all of his chakra and then if he revived someone, he wouldnt have died as Konan herself told "At his CURRENT chakra level, if he uses that jutsu he will die" (when Pain revived everyone in the leaf). Even if he would die using it, he should have used as it was his ultimate goal to to protect 'those two'.

6. According to Konan in the above point, you don't die if you use it at high chakra. But what's worth noticing is how Konan knew about that jutsu and its working. And by this - "At his CURRENT chakra level, if he uses that jutsu he will die"...we can infer that Nagato might have used it before and that's how Konan would have known how much chakra was needed. And even if we say Tobi told him of the working, chakra usage should still be unclear. Unless it's a dubbing fault, there's no other explanation that I can think of.

7. When Orochimaru revived all the Hokages, why did he revive everyone else in their young and strongest state while 3rd Hokage was still old? Reviving someone in any state has no effect on their memory as its clear from Madara's revival. Reviving 3rd in his young state would have been better for both choices - protect or destroy the leaf as he would be even stronger.

(1) Sharingan can copy chakra natures, I believe. Also you can have multiple chakra natures, most ninja are just good in 1 or 2 and absolute trash in the others.

(2) Summoning Jutsu uses a seal, similar to how you can summon ninja tools by touching a seal.

(3) Tailed Beast's are 100% pure chakra, so Kurama's soul is likely just a huge mass of chakra that mixed with Minato during the RDS.

(4) Itachi is like Snape, except on a tighter leash. Kisame follows him everywhere, he likely had very little time to drop info.

(5) Rinne Tensei kills the user no matter what, that was an issue in translation. He probably realized Yahiko wouldn't want to come back in that fashion, with his friend dying.

(6) Rinne Tensei kills the user when used. It's in a databook. Obito only survived because of the Juubi's shell, if I recall.

(7) You can only Edo Tensei someone at the point that they died. Madara is an exception because Kabuto performed specific experiments and jutsu to bring him back younger.

1. It's never shown and if it were true Madara, Itachi, Obito and many others would too be able to change chakra nature, i.e. Every Sharingan user would be known as copy ninja but that's not the case. Only Kakashi could do that so it makes much more sense if you relate to his genius in controlling chakra flow and changing chakra nature. And unless you have Kekkei Genkai, you can't naturally have more than 1 nature.

2. Ok.

3. Seems true.

4. Atleast he could have sent a crow.

5. That goes super contradictory to what he believed.If that was the case, why would he carry his body around. He wanted to protect him at all cost and I don't think he would even have a second thought if he loved (friendly) Yahiko as much he said he did. He was even his 2nd reason of pain.

6. Agreed.

7. If that was the case, how were 1st and 2nd were revived in their prime. I don't recall anyone killing either 1st or 2nd and all the other kage. Even Raikage's dad wasn't killed.

@zenux:

(1) This is disproven by the entire Shinobi Alliance using a Dotun Wall.

(4) Yeah, Kishi didn't really capitalize on this.

(5) He probably knew Yahiko wouldn't want to be revived after sacrificing his life to save his friends. ESPECIALLY when he sacrificed specifically FOR Nagato. Would be like a slap in the face to revive him.

(6) We don't know how the 1st died, so it's possible he died just like he is. We know Tobirama died at that age against a unit of ninja. Same goes for the other Kage, we don't know how they died, so it's plausible they died as is. Somehow.

(8) He probably didn't want to risk Tobi countering it somehow. Itachi thought Tobi was Madara - And with Madara's reputation, he probably didn't want to risk wasting the Koto, in case Madara had some secret counter.

@zenux: im gonna answer your question about Orochimaru since it wasn't addressed. When he switched bodies he regained the use of his arms.

@shadowchaos: Arms yes, jutsu no.

1. That was the weakest form of Earth style. Shikamaru specifically asked for a jutsu that was so easy that everyone could do it. Kakashi and 3rd used much complex jutsus. Fireball, water dragon, chidori, head hunter. That's called being able to use it. Dotun wall was same (as per casting level) as clone jutsu, no matter what your chakra nature is, you can do it. Name any other who can do it.

5. Seems logical.

6. Considering the fact that 1st was called God of all shinobi and the best ninja, he didn't die from a defeat. He could heal in an unimaginable way so he couldn't have died of a disease either. He later got married and had a grandchild and taught her how to gamble so she must be about 10. By this time he would be pretty old no matter how you think of it. Same as 3rd, as it's the same case. So it's most plausible to assume that he died of an old age.

8. Yea true...I too thought of that that's why I edited my question again.

I honestly believe that Kishimoto simply stoped giving a shit all together after the Pain arc

@_mongul: i don't think his jutsus were really sealed. I think it was just his arms.

@shadowchaos: Nope it was his jutsu as well. At the end of the manga he confronts the Reaper and takes his jutsu back.

@_mongul: hmm don't remember that. Maybe it was all the jutsu he had learned up till then. So he had to relearn them

@shadowchaos: Uh no that's still wrong, because he was unable to use any jutsu (aside from summoning) for the remainder of Shippuden, then when he got his arms back he could use them again.

@_mongul: then who knows.

As for Edo Tensei my theory is that it brings the target back in the condition the user is most familiar with. Hince why Hashirama and Madara were brought back in their prime. Since most stories and legends would have them being in their prime. While Orochimaru was familiar with old Sarutobi. For obvious reasons.

Neither Orochimaru nor Kabuto had seen either Hashirama or Madara. So how did they bring out both in their prime? If just hearing and reading was true, then Orochimaru could have brought Sarutobi too in prime as he was with him since he was a kid. He even saw him unlike those two.