Khailin
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Okay, so, I know how some people are resiliant to "Tobi isn't Madara" threads, so please do not read/comment on this thread if you are one of these. I am making this thread for people to ponder on, and I don't need haters. You have been warned.
Okay, so, I've been thinking (as I always do), and I've come to a conclusion about Madara (were you expecting me to say Tobi?). But before I get into my theory, I'll begin with facts.
Fact one, Tobi has never taken his mask off to the reader, only to characters, who have refered to him as Madara (ie. Kisame). Second, Zetsu is of Madara's creation (You must be registered for see links). Third, Zetsu can copy anyone near perfectly (You must be registered for see links). Fourth, Tobi has never been seen with Madara's EMS. Fifth, Tobi can remove his arm, leaving a white substance at the joint (You must be registered for see links). Sixth, Tobi helped Itachi kill off his clan. Seventh (there's a lot, aren't there? xd), Tobi has a mass collection of Sharingan at his disposal (You must be registered for see links). Eighth, Zetsu calls Tobi "Tobi", despite everyone else calling him "Madara" (You must be registered for see links). Now onto the good stuff.
But, before that, a lot of my theory branches off of this one.You must be registered for see linksTo understand most of my theory, you may want to read that (or skim it to get the jist of it). Now, with that settled, I'll begin.
How can a human, even the most powerful Uchiha in existance, live for as long as Madara claims to have? This is a major factor in this theory. Espcially the word, "human". You see, what first turned me to my theory is the episode (which I linked above.You must be registered for see links). Madara takes off his arm, and leaves the white clump at the end of it behind. How interesting. And then he get's it back relativly quickly afterwards. Hmmm... Who else can detach their limbs and then regrow them...?
After thinking of this, I remembered that theory I mentioned earlier. Now, this theory says that Madara created Zetsu (or at least White Zetsu) out of Biiju chakra and Hashirama's DNA. Now, this is instrumental to my theory, and I expect that a few people may be able to put it together from here, but I'll continue for those who still need a little help.
So, since Madara created Zetsu, Madara knows exactly what Zetsu can do (unless Zetsu was a mistake, but I'm ruling that out for the time being). A question arises from this; why? Why would Madara take the biiju's chakra and Hashirama's DNA to create Zetsu? What's the purpose to it? The purpose to it is that Zetsu isn't human, and therefore, isn't bound by the rules of longevity (how long a human can live before they die of old age). This gives Madara an advantage, in a way.
Now, using the fact that Zetsu won't die of old age, and can create spores so he can't die (in a way), you have to take into account another ability of Zetsu; the fact that he can copy a person to a point. Now, Madara knew that he would die (as all people do; even the Sage), so he created Zetsu to solve this problem. By having White Zetsu make a clone of himself, and having that clone touch Madara and transform into him, by the time Madara died, there was a Zetsu clone of Madara. He also implanted his EMS into Nagato, an Uzumaki with exceptional chakra, so he could develop the Rinnegan (Madara couldn't take it for himself, as he was about to die, and he thought that Zetsu would have the EMS. This was ensuring Zetsu the Rinnegan; essential to the plan. There's a theory saying that the EMS and an Uzumaki can somehow create the Rinnegan; I'll share it sometime if I can find it). But there was a problem. The cloning process wasn't perfect...
Zetsu can't copy Kekkei Genkai (fusing with Samehada wasn't Kekkei Genkai; it was more of a Hidden Jutsu); if he could, why not just make millions of copies of every powerful ninja with epic Kekkei Genkai? Therefore, this Madara copy didn't have a Sharingan, which was a major problem for Tobi (the name Zetsu had given to the Madara representation of himself). So, Tobi went and killed an Uchiha, stealing a Sharingan from him/her. Unfortunatly, Tobi quickly realized that his Sharingan wasn't going to be enough if he were to carry out Madara's plans that were left with him (this realization came after losing to Minato). Then, Tobi found Itachi...
Tobi and Itachi worked together (or something like that) to devistate the Uchiha clan. Afterwards, Tobi took the Sharingan from the dead Uchiha to try and recreate Madara's EMS, but to no avail. But after learning that Danzo and Orochimaru were also collecting Sharingan, he wasn't about to release all of his collected Uchiha eye's to the one who had given the order to kill their owners; he's obviously planning something. This made Tobi weary of Danzo, even to the meeting at the bridge, where he found the purpose of the sharingan Danzo had collected.
After learning that Itachi had left his little brother alive, he waited for his oppertunity. After Sasuke killed Itachi (I know that Sasuke didn't actually kill him, but that's the easy way to describe it, so deal with how I adress it in my theory), Tobi took his chance, keeping his cover as 'Madara', and manipulated Sasuke's emotions so that Sasuke would work with him, and eventually ask Madara for Itachi's eyes; for the EMS Zetsu could never recreate.
Tobi's plans now are to use his last Sharingan to it's fullest and then take the other Rinnegan (You must be registered for see links). After having two Rinnegan within himself, he plans to take Sasuke's EMS and enfuse his Rinnegan with it to create an augmented Sharin/Rinnegan combo (as seen on the moon as Madara explained his plan.You must be registered for see links).
But, wait... Tobi could teleport and phase through objects without Madara's eyes. What's going on here? Well, Zetsu can phase through things. But, he can only phase through plant-like materials. Or can he...? What if Tobi is the original Zetsu, and the White Zetsu we see now is one of the inferior clones, and the original could phase through more than plant-like materials? Or maybe it was a Sharingan ability, which he got from the random Uchiha he killed for the first Sharingan. Have we seen him phase through things since he used Izanagi and sealed away the one eye....? (If we have, then it's probalby a superior Zetsu tech.) And as for his teleporting, most likely also a tech. from a Sharingan (don't rule it out; Shisui could mind-control with a 3-tomoe).
Now, what is this theory missing....? I got side-tracked with the Zetsu/true Madara story I was telling..... xd Well, let's go back to the 'Zetsu was a mistake' thing. How can you accedentilly merge the biiju's chakra and Hashirama's DNA in the exact conditions needed to grow a Zetsu. If you ask me, it's highly unlikely that Zetsu was a mistake, and therefore Madara knew what Zetsu could do (with the exception of the Kekkei Genkai thing).
In conclusions, this theory basically says that Madara is and isn't who he says he is at the same time. It explains the ''I'm a shell of my former self," line, and Madara(and Tobi)'s mysterious connection to Zetsu. It also answers this; we saw that when Danzo was merged with the first (somewhat), his arm was augmented, yet Tobi displays none of this. This could be due to Zetsu's ability to easly absorb and replicate DNA, thus making a Madara/Hashirama combo easily, while retaining the physical essence of Madara only. It also says that the 6th coffin could be Madara, even though I doubt Kabuto knows about this, and believes that Tobi is Madara (as most everyone does). (It seems the only question I haven't answered is "What are the other three paths?" I'll tell you as soon as I figure it out. xd)
Now, for those of you who survived this majorly long theory, I'd like to ask; did I miss anything? Is there anything you didn't understand? Holes in my theory? I would like to defend it as much as possible, as I believe strongly in this, and I would like to know if I missed anything in making this theory iron-clad. So, questions? Comments? Concerns? Getting your stick ready to poke holes (xd)? I'm ready, so let's hear it! (It's long, I know...... X__X)
Nice, man. I never thought of those subtle details, but your theory really makes sense when you add it all up.
brothers 
