Since I started all of this, I might as well respond. Maybe chakra is connected more to one's soul than to one's physical body, which would explain how Tobi is able to take the Nine-Tail's chakra from the Gold and Silver brothers. Of course, this would then raise plenty of questions about chakra flow within the body - the whole basis of Neji's techniques would become suspect, for example.

As for the original point I was positing, I guess I should have been more clear. My dilemma had more to do with what happens in Chapter 490. The Nagato shown along with the others simply seems to be a corpse. It certainly isn't animated like other Edo Tensei ninja are. The question I was trying to resolve was whether the Nagato in 490 was an Edo Tensei powered vessel or the actual corpse of Nagato. The problem with the "actual corpse" side is that Tobi needed to go find the body of Nagato afterwards to retrieve the Rinnegan. On the other hand, the "Edo Tensei explanation" doesn't really seem to fit either just based on the appearance and inactivity of the body in the coffin (yes, it does have the same cracked paper look, but that could just be simple decomposition). The Nagato shown in 490 appears to be much different from the Edo Tensei Nagato shown later. As such, there is an odd discrepancy that suggests a plot-hole here.

I'm not saying you don't have a good point, but your comparisons to the rinnegan and the 9-tails chakra may not hold. The rinnegan that is ressurected with its user isn't actually real, just as Itachi's mangekyou sharingan couldn't have been real because they were already in Sasuke's eyes. They are a result of the user's soul and chakra activating said kekegenkai in a body molded from their DNA.

There is one plot hole you definitely did open my eyes up to, though: how the FUCK did Kabuto revive Nagato?

the body of nagato in the coffin was an ET resurrected nagato bc at tht time kabuto had already resurrected him and all the others he showed but he had them basically in a sleep mode there have been scenes where kabuto was able to put the ET resurrection back in their coffins as he sees fit and they then become inactive so most likely it was not the real nagato just a
ET inactive body with his soul attached

^ But he would need Nagato's DNA to even resurrect him. To top it off Tobi had to hunt Konan down to find Nagato's body... Did Tobi not think: huh wait a second, maybe I should ask Kabuto where the fuck he got that DNA so I can, um, not get my body parts blown off of me and resort to using Izanagi to save my ass from an otherwise seriously unnecessary fight?

Keep in mind that in order to revive NAGATO, he needed NAGATO'S DNA, none of the six paths of pain would suffice and that's the only face any Akatsuki member saw of Pain so Orochimaru's time spent in Akatsuki can't account for that. The body was taken away by Konan right after Nagato revived the Konoha members he killed (Jiraya somewhere in the heavens screaming: you forgot ME you fucking idiot!!!)

As long as Kabuto has been around Orochimaru you don't think he had a DNA sample of Nagato from a prior battlefied? If Kabuto could resurrect Hanzo then it's obvious he could have gotten Nagato's DNA back from when he fought and killed him. That is not a plothole......

Also Tobi went to get Nagato's body because at that time Kabuto hadn't approached him about teaming up for the war so he had no idea that Edo Tensei Nagato existed yet.

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