In no particular order:
- Hashirama was said to be the most powerful ninja of his time, and immortal, how the f**k did he die?
- What the hell does the Rikudou sennin's prophecy mean?
- Can Naruto combine SM with Kurama's power?
- Who is the person Sasuke want's to speak with who knows everything?
- Who are the people Orochimaru referred to as "them" when Sasuke shows him the scroll?
- How did Rin die?
- What happened to Obito after he was crushed that changed him enough to become Tobi?
- Who made Zetsu?
- If Orochimaru and Jiraiya have trained with a sage, did Tsunade do the same?
- Does Naruto still have an unknown ("that jutsu"), or was that just the ability to place the Kyuubi under a new seal?
- How did Madara gain the Rinnegan?
- How did Nagato get his Rinnegan?
- How does the partial chakra given to Naruto from the other Bijuu pertain to the Rikudou sennin's prophecy?
1 It was never said Hashi was immortal, just very OP
2 essentially that whoever the chosen one(s) are (Naruto/Sasuke [if there are two of them like the sages kids]) would bring peace to the world.
3 No he can not, that was explained by Bee and the Hachibi, because of how the exchange of chakra works between the bijuu and the Jinchuriki sage mode cannot be used.
4 More than likely madara, because sasuke freezes up and gets all weird whenever Madara is brought up, for example when Juugo was talking to the bird and it said edo madara was still around.
5 not sure, probably the sages that Oro trained with. But it may also be related to the rinnengan (Hence the chapter title being "The Third Power" which is what the rinnengan is)
6-8 so far the only ones without a logical answer
9 probably not, otherwise she proabably would have used her sage abilities against edo madara. plus, Oro summons snakes, probably trained with snakes, Jman summons toads, trained with toads, Tsunade summons a slug. if she trained with a slug sage, i hate life. also, tsunade is just retarded anyway.
10 Probably not, if it existed it would more than likely have been used against Tobito by now
11 by fusing his dna with the first hokage's (senju and uchiha dna is needed to activate it)
12 according to Tobito, he gave the rinnengan to Nagato, but because of the timeline that doesn't exactly work, i'm sure it will all be tied together. Maybe that was because he was making people believe that he was madara, and madara actually did it.
13 extra chakra means extra power. extra power means extra bad-assery, which means extra ass kicking. Probably to help Naruto achieve a goal of peace in the shinobi world.
I don't mean to be rude, but many of these things had been explained and/or hinted at in the manga. It's easier to just take the time and read it