I posted a similar thread to this a while back, but I’m going to be taking a slightly different stance in this thread.
First, I just wanna say that I know that Six Paths of Pain loses to all versions of Obito. You could argue that this Pain can beat Kid Obito since Kid Obito has fewer speed feats than his older self, and Pain is one of the few opponents that doesn’t get immediately decimated, but Kid Obito would still likely come out on top.
Pain’s primary weakness against Obito is the separation of the Paths.
However, I do believe that a healthy, PRIME Nagato, can defeat Kid Obito and Orange-Mask Obito with relative ease. I also believe that Prime Nagato can give White-Mask Obito (without Jinchuriki) a run for his money, but would end up losing. (White Mask wins with mid-high difficulty, due to his access to the Rinnegan’s abilities as well). All the paths in one body makes for an amazing defensive core as well as extreme versatility, something that the Six Paths of Pain did much less efficiently.
(I don’t consider Kid Obito to have the 9 tails’ power, since he could not summon it at any given point in time at will, like Madara could. He also lost it in the same battle he gained it.)
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The way many battles end with Obito winning involves his immunity to various attacks and techniques, his Kamui is op hax as I’m pretty sure everyone is aware of. But I’m gonna save talking about his Kamui for last and I’ll start off by talking about how Nagato is essentially “immune” to all of his other abilities, just to get it out of the way.
1. Obito’s Fire Release and Wood Release - Nagato is able to nullify both Releases as they are ninjutsu and are made up of chakra: the Preta Path can absorb ALL chakra. Even in the case where Nagato is unable to use Preta Path for whatever reason, a Shinra Tensei would also deflect/dissipate either Release.
2. Ninja weaponry - This technically involves Kamui, but I don’t think it really counts as Obito using it in its most viable way. He has shown the ability to shoot out shuriken, kunai and Fire Release (Fire Release is prevented from the 1. explanation). As for the ninja weaponry, Nagato can use Shinra Tensei to deflect these, use his summonings like the Panda to block them, protect himself with his Asura armour etc. These things aren’t really a factor against Nagato.
3. Taijutsu - Obviously, we know Obito is very skilled in CQC; he has to be skilled, since it is how he is able to end many fights as efficiently as possible, in conjunction with Kamui. But, it wouldn’t be too easy against an opponent like Nagato, thanks to his Asura Path extensions preventing Obito from getting too close, and the shared vision Nagato would have available to him through his summonings and the King of Hell.
4. Genjutsu - This most likely wouldn’t work on Nagato, as the Rinnegan is highly resistant to visual genjutsu. (The only genjutsu that has worked on a Rinnegan user was a SOUND based one, Frog Song.) Even if Nagato was caught in the genjutsu, his shared vision with his summonings would alert him of this straight away.
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5. Kamui
Right, now onto the part that actually matters.
As seen by the above analysis of Obito’s other abilities, the only way Obito can possibly beat Nagato is through his use of Kamui. In order for Obito to use Kamui, he has to come into close-quarters with Nagato so he can begin to suck him into the dimension. BUT, Obito has to stay materialised in order to pull someone/something into Kamui. This means that Obito will be vulnerable to the Asura Path extensions that Nagato can create. These extra limbs, wires and mechanisms can be extended quite a long way, which would keep Obito too far from Nagato’s actual body in order to pull him into Kamui.
Obviously, these Asura extensions aren’t going to stop Obito, since he would simply dematerialise to move closer to Nagato. However, this leads onto Obito’s other problem: Soul Steal. The moment Obito materialises to suck Nagato into Kamui is the moment Nagato grabs his soul. This does NOT mean that Nagato wins at this point, since Obito would dematerialise before Nagato fully rips his soul out. However, it DOES mean that Obito would also fail in sucking Nagato into Kamui. The point of me detailing this exchange is to show how Nagato can utilise the bluff of ripping Obito’s soul out to avoid being pulled into Kamui. And for those who would think that Obito would continue to suck Nagato into Kamui despite being grabbed, Nagato would still have Obito’s soul gripped in his hand, meaning that Obito’s soul would be pulled along with Nagato into the Kamui dimension, indicating a defeat on both sides.
Just to add on, I think Nagato has exhibited enough speed feats to be able to keep up with Orange Mask Obito, along with his shared vision and his legendary sensory abilities. A crippled and white-haired Nagato was able to keep up with Killer Bee in close quarters. Before Killer Bee threw the Lariat that led to his chakra being absorbed, Killer Bee threw an initial punch to which Nagato DODGED easily. From this, we can understand that a Prime Nagato, a Nagato that would be in even better shape than when he absorbed Bee’s chakra, would perform and react even better. Obito boasts just as great speed feats, with him REACTING to the Raikage’s punch and avoiding Ohnoki’s dust release, quick enough to dematerialise on both occasions.
With those feats being said, we must acknowledge that Killer Bee and Raikage HAVE to be at similar speed levels in order to synchronise their Double Lariat, and Killer Bee was in his Tailed Beast Cloak Mode against Nagato, which would have boosted his speed and power. From this I can comfortably say that a Prime Nagato would not be easily blitzed by Orange Mask Obito, especially not with his Asura armour, wires and shared vision.
Hence, this battle would be a long-winded stalemate. Nagato is an absolute chakra monster whilst Obito is essentially half Hashirama cells. Additionally, Nagato is exerting little to no chakra in this fight, since his techniques he would use against Obito are mostly defensive, and any contact with Obito would actually restore chakra through the Preta Path.
Now, what would turn this battle into a WIN for Nagato, would be his use of Shadow Clones. Nagato has shown the ability to use Shadow Clones from as early as the Original Akatsuki, which would prove instrumental against Obito in a fight. All Nagato would need to do is create at least 2 shadow clones (he can obviously make more given his monstrous chakra level) to compensate for the lack of bodies that he has as Prime Nagato, and not the Six Paths of Pain. This essentially leaves Obito near helpless, since if Obito attempts to suck Nagato into Kamui and succeeds, he automatically loses the fight. By doing this, he will have forfeited his ability to go intangible, as he would be attacked in the Kamui dimension by either the real Nagato or one of Nagato’s clones. Nagato wouldn’t even need to rip Obito’s soul out; if either Nagato stabbed Obito with a chakra rod, Obito would be unable to utilise any of his techniques properly, and could then be dispatched with minimal difficulty.
Also, if real Nagato was the one who was sucked into the Kamui dimension, Nagato’s clones would be able to reverse-summon Nagato back through the Animal Path.
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6. Izanagi
Now, I haven’t forgotten this ability. Obito would obviously use this when caught up in the dire situation shown above, but all this technique would do is save Obito from death, not secure him the win. When used against Konan, he appeared directly behind her and then stabbed her with an iron pipe. Against Nagato, something like this wouldn’t work. Nagato’s shared vision, his close proximity to his other shadow clone/s and his godly sensory abilities would allow Obito to be noticed quite quickly. This was the same with Danzo, he simply reappeared a certain distance away from Sasuke, and was immediately detected by Karin. Nagato’s sensory skills are LEAGUES above Karin’s, meaning that Nagato would be able to sense Obito fairly quickly.
Obito might be able to catch Nagato off-guard and dispatch one of his clones, but this is highly unlikely given the aforementioned reasons. Obito would most likely use his ninja weaponry or Releases disrupt the shared vision of the summonings since they have no way of dodging these attacks. But once this has been done, Nagato would then know for certain that Obito is not dead, and then Obito would be back to square one, where none of his techniques would help him against Nagato and his clones.