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At large capturing naruto was of no benefit to madara for the most of the series. Even when pain was actually sent to do the job this was done under the assumption that sasuke would first succeed in capturing killerbee. Lets get serious, what exactly would have been accomplished by capturing naruto earlier? Could they kill him? that was largely impractical as they would have had to capture the resurreccted kyuni, wherever he might reappear, and that is assuming a village did not get to him first. Could they seal the kyubi? Of course not, the manga was very clear in explaining that naruto must necessarily be sealed last. Was it a good idea to keep him imprisoned? I have my doubts about that..... As they are dealing with ninja escaping is always a remote possibility and in this case there is a chance that naruto might have even released the kyubi wherever they could imprison him. In the early stages of the manga akatsuki had to even concern themselves with other jinchuiriki which they could in fact seal within the statue. Why waste time and resources over a jinchuiriki they could not seal and on top of that was protected by the most powerful village when on top of that there were 8 other creatures in less powerful villages which they could seal?
He could basically lay on a beach and take a sun bath with the whole ninja world trying to assassinate him and it wouldn't make a difference. It probably takes a special power to fight a special power, and it's seemingly not something anyone possesses at the moment.
On top of that he can teleport wherever pretty fast... Just imagine, how easy it would, to kidnap all the tailed beast alone like this... All he'd need would be a little detail and he could pretty much do it single handedly in 1 night, there is no need for Akatsuki... It's quite the stupidity that he's this powerful, yet, he relies on Akatsuki.
If there is a reason for Akatsuki, then it's bad that Kishi doesn't explain it beforehand, hell, they're almost all dead and goners and it's still not explained... Damn it Kishi .. The story is suffering from it.. and it's true, why didn't Naruto not get captured earlier when he could capture them all alone easily...? At this rate, Madara may end up as the most stupid main villain ever... No offence, but this is really crappy.. Madara could have resurrected the Juubi, ages ago, yet, he didn't... No offence, I just don't agree that there is a logical explanation around this issue, it's a really big one at that..
I don't think madara could have just appeared and taken the biju.... For one thing, he has to know exactly where they are from the get go. For another, the jinchuiriki have at large been powerful shinobi. His teleportation is fast but I don't think it is quite as instantaneous as you make it out to be. We always see that spiraling around his eye, it does not seem to be quite as fast as minato's kunai thingy. Moreover, the villages usually take fairly good care of their jinchuiriki. Madara would take a huge personal risk if he exposes himself so easily. Not to mention that his intangibility is flawed. If his gets into a fight he can't just be intangible throughout all of it. One thing we did learn from konan is that madara can only remain intangible for 10 minutes at most. Izanagi is an option but in turn he only has 1 shot at that.
We also have to consider akatsuki has not dedicated itself solely to capturing biju. All the villages hired akatsuki for a number of jobs. Madara couldn't have possibly exposed himself to such a thing nor he could have carried a significant number of missions on his own.
It's actually been the opposite, with the villages not taking very good care of their Jinchuuriki. Kirabi and Kushina were the only ones we have seen that were treated well, because of who they were connected too. All the others have been shown and implied to have had a terrible life growing up. Heck, we were told that two of the Jinchuuriki were handed over with no problem to Akatsuki and at least one Jinchuuriki had already left his village to travel. Iwa was more concern about being seen weak then actually losing their Jinchuuriki and Kumo didn't shown any reaction to losing Yugito.
From all that we've been told, it wouldn't have been hard for Madara to figure out who the Jinchuuriki were. He would simply have had to look at anyone connected to the Kages and/or whoever was an outcast. After that, fighting shouldn't have been much trouble, since he simply needs to lay a hand on them. Regardless of their strength, avoiding Madara touching them wouldn't have been extremely hard. And that's assuming he simply didn't take them by surprise or when they slept.
It's a possible plot hole but I think there are potential reasons aside from the obvious impact it would have on storyline.
1. Kakashi / Yamoto were on were on full alert when Madara appeared at the Hotel - it may not have been possible to simply warp in and out without risk. Naruto for one would not let things be so easy. We can also assume there was some sort of barrier around the hotel which alerted them of Madara's appearance.
2. All the previous Jinchuuriki's were beaten half to death before being taken for extraction - Naruto was in good shape, the assumption is that this may have caused issues at the other end. Naruto was credited by Zetsu as being stronger than Sasuke after he defeated Pain - he's no push over. If this was the case, why does Madara even need the Akatsuki? He could simply warp over to every Jinchuuriki's location and capture them with risk. He seemed to know Naruto's exact location (as he knew Sasuke's; although this could be the help of Zetsu) therefore finding the other Jinchuuriki's would not be beyond his abilities.
Risk vs Reward - perhaps the risks were too great and therefore he decided not to. At this stage he didn't have his Rinnegan either so he wasn't at full strength. Being able to become intangible or warping around are very much defensive abilities and not suited for attack - Konan pretty much had him sussed had it not been for Izanagi.
There is a difference between how the villagers treated the jinchuiriki and how the top brass treated them. The regular villagers of the different countries were at large hostile to the jinchuikiri but that is not to say the to brass the of the villages were the same way. As far as they were concerned the jinchuiriki were their weapons of war and should be available and checked on at all times. I very much doubt they just neglected them. Obviously they would have been left to their own affairs within the village but as we saw with naruto, killerboo or gaara their movements and missions would be carefully coordinated for the most part.
Tobi could have also been focusing on building up Akatsuki and getting revenge on Konoha and Uchiha to worry much about Naruto at that point. Tobi most likely didn't plan on Naruto becoming as powerful as he is now and after talking with and converting Nagato, Tobi is probably interested in Naruto. I think Naruto convinced Tobi to turn the whole Naruto thing into Naruto vs. Sasuke, Senju vs. Uchiha.
for the story's sake.if he had been captured,the story wouldn't have been like this.
Other than that, we have no reason to actually believe even kirabi was treated well by the villagers at first. Odds are the villagers neglected him just as much as naruto or gaara were but in turn he at least had a proper loving brother and people to fall back on. I don't think kirabi was outright loved from the beginning, IMO he came to be loved with time as is the case with naruto.
Just because they were provided for doesn't change that they were neglected. Material goods are hardly a substitute for human affection. We saw that they were basically left on their own the majority of time. Gaara at least had Yashamaru, but we saw how that turn out. Who raised Naruto is unknown, but considering he didn't make a connection with anyone until Iruka, that's says quite a bit. Kirabi wasn't treated well by the villagers, we were told that by Motoi. But the simply fact he had someone caring for him right off the bat, not to mention probably some relatives considering Kumo seems to have kept the Hachibi within that single family. He had someone to back him up physically and mentally, something Naruto and somewhat Gaara lacked.
Anyway, the point was that apart from Kirabi, Madara wouldn't have had much trouble grabbing any of the Jinchuuriki, including Naruto and Gaara. They were left on their own so much, that by the time anyone could realize something was up it would have been too late.
So konoha's top brass had a sort of duty to provide naruto with love and human affection? Now that is just plain dumb, why would they bother with such a thing? As far as konoha's government goes we have no reason to believe naruto was treated differently from any other orphan in the village. Naruto was just unlucky in that he had a monster inside him that was hated by everyone and unlike kirabi or gaara naruto did not actually have a family of his own.
Now, the issue here is that you are assuming the jinchuiriki could not have possibly fought back against madara which is quite dumb. Even danzo's subordinates gave him trouble, can you imagine the guy constantly sneaking into villages taking on biju? I very much doubt there are no protections that can be used against space time jutsu either, specially if for every captured biju he reveals more and more of his own abilities. Even if systematically fighting to the death with each individual jinchuiriki was something doable for madara, doesn't it still work much more easily for him to have someone else do it for him? I would think that between him having to fight to the death with 9 jinchuiriki and having someone else do it, the latter is far the better option. Even sneaking in while they sleep could have been difficult, these are trained shinobi who are trained to deal with every sort of situation. These guys are usually sensitive enough to notice people hiding from them from reasonable distances, I doubt things would have gone so smoothly. Not to mention it is not like madara could just teleport to them, he would have to start by knowing where they are. Its not like he can feel ki's and magically teleport to where they are, the gruntwork is not done magically done by teleporting. At the very least he would need zetsu to put spores on the targets in order to be able to know where he is at all times....
Of course they had a duty, since they actually knew who's child he was and why exactly he was made into a Jinchuuriki. Considering how revered Minato was, treating his child with a little love and affection would have been the least they could do. Not to mention they should have also known about the whole "feeling up their heart" thing, that the more affection and loved they showed him, the stronger he could become. As for how other orphans were treated, that was apparently the point of Root, to take in and train those orphans. Considering how things have gone, probably would have been a good place for Naruto to be sent. And having actual family wouldn't be a factor. Kirabi wasn't at all related to Ee, yet they became as close as brothers despite him being a Jinchuuriki.
I do doubt the majority of Jinchuuriki could have fought back. Because all that Madara needed to do is lay a hand on them and he would have had them. No extend fighting in the middle of the village or anything. The only reason Fuu and Torune gave him trouble was because they knew what he was capable of and had each other to rescue themselves. We're talking about probably the two strongest Root members and the most they were able to do was make it so Madara got damaged when he touched them. Heck, Minato had trouble with Madara and only manage to win due to his own space/time technique. So simply escaping Madara isn't gonna be a cakewalk for any ninja. Now factor in that depending on when and where Madara went after the Jinchuuriki, and odds are he wouldn't have to worry about them putting up any sort of fight. Just look at the current situation. So far Kirabi is the only Jinchuuriki shown to have been trained from a young age, though Yugito could also be included in that.
Madara was able to get within touching distance of both Minato and Fuu before they knew he was there, and Fuu was an actual sensor ninja. So there's no reason to believe that Madara couldn't get just as close to a sleeping target and warp them before they could fully react. As for knowing where they are, it's still unexplained how he's able to find people though he has been able to locate various people several times now even though they couldn't have been covered in Zetsu's spores. Even discounting that, some simple research would have allowed him to learn who and locate his target. He was apparently able to sneak in and out of Konoha several times without anyone catching on.
My only best and real answer and I know people are going to flame on this.
This movie is about Naruto and that's why he wasn't capture long long time ago.
I'm sure y'all know this, but some of you haven't accept the truth yet.
For me Naruto and Sasuke has been a Part of Madaras Real Plan and here are some Proof:
We have seen what Madara Eye Moon plan is when he explained it to the kages here:
And again this page: http://www.mangareader.net/93-56935-...apter-507.html
We can Clearly see that Madara has not relevead The *Eye Moon Plan* That is differend then what he has explained but some other plan that Kisame has confident in.
Back to Madara Where we see his Old Mask and Cloths: http://www.mangareader.net/93-54942-...apter-500.html
We see old Mask that seems to resemble his Time-Space Jutsu and it looks its not finished yet.
And his Prediction that Naruto has the Nine-Tails under Control: http://www.mangareader.net/naruto/545
I believe he can predict the future like the Eye like the The Eye Pyramid