(DISCLAIMER: This is just a theory, it's not entirely complete and I can't prove anything, but if my theory is correct, I'll spoil many of the biggest plot twists in Naruto. And I have a LOT of confidence in this theory. I've thought about it for hours and carefully checked my sources. So read with caution.)
There has been a lot of speculation about the identity of two of the members of Akatsuki- the leader and Tobi. Several people have argued that the leader is really the 4th Hokage, while other insist that Tobi is really Kakashi's old friend Uchiha Obito. These people are usually ridiculed -I myself only yesterday spent quite some time arguing that the Akatsuki leader couldn't POSSIBLY be the 4th Hokage- but today I had a revelation that finally tied everything together and made it all make sense. Although I haven't seen the whole puzzle yet, it's as though I found the key piece that lets me fit all the other pieces together.
(SECOND DISCLAIMER: I don't know if anyone else has suggested this theory before, but I personally haven't seen anyone do so. My apologies if anyone has.)
I will present my theory in 3 sections:
THE AKATSUKI LEADER IS REALLY THE FOURTH HOKAGE?
People who argue this theory usually base it on the fact that the leader has spiky hair, and so did the 4th Hokage. This is not a good basis for an argument. On the other hand, there are a number of points against that are rather notable. Firstly, the Akatsuki leader does NOT look much like the 4th Hokage- although they both have spiky hair, the 4th had long spiky golden hair, almost a mane, while the AL has short spiky auburn hair (as seen on the cover of chapter 317- he's standing up the top). Additionally, the 4th didn't have the facial markings/piercings on either side of his nose that the AL possesses. However, all points along this line or argument are more or less irrelevant, as it has been many years since the 4th was seen and in any case, a skilled ninja's appearance is more or less up to their will. The resemblance is still enough for it to at least be worth considering, even if it is not enough alone.
There are other factors to be considered. The AL's most significant jutsu, the 'Sealing Technique: Illusionary Dragon Nine Consuming Seals' (the one used to extract the bijuu from the jinchuuriki and seal it within the statue) has notable functional similarities to the 'Dead Demon Consuming Seal' supposedly used by the 4th to seal the kyuubi into Naruto. It is not beyond the bounds of possibility that the former is a deriviative version of the latter meant to SAFELY extract a bijuu (or, in the case of the Sanbi, break it down) and seal it without anyone losing their life. This would explain why it takes several S-ranked shinobi 3 whole days to complete, if they are performing a jutsu that would normally be fatal to a single shinobi performing it hurriedly. Additionally, the AL has a notable knowledge of Konoha's 'Will of Fire' which he explains to Hidan. Finally, the almost excessive mystery sustained around the AL's identity seems to indicate that he is a character known to the series, which is why his identity is being kept a careful secret for now.
However, the case against can still be strongly built on the fact that the 4th Hokage is dead. Dead as a doornail. Although it might be possible that he survived the Dead Demon Consuming Seal SOMEHOW and faked his own death, he had no motive for doing so. So realistically, the 4th is dead. Additionally, the 4th's personality in NO WAY overlaps with that displayed by the Akatsuki leader: one is the most noble shinobi Konoha has ever known, the other is an evil bastard with plans for global domination. This is an ALMOST unsurmountable obstacle for the theory to overcome- almost, but not quite...
TOBI IS UCHIHA OBITO?
There is actually a lot more material evidence for the idea that Tobi is Obito than there is for the 4th/AL theory. Tobi's short, spiky black hair is actually virtually identical to Obito's, he wears a mask with one eyehole on it (on the right; Obito gave his left eye to Kakashi), his goofy, laid-back, carefree attitude resembles Obito's (who has been described as his team's version of Naruto) and their names are VERY similar. However, this theory faces the same impressive obstacle as the 4th/AL theory: Obito is even deader than the 4th. Unlike with the 4th we actually SAW Obito die in the Kakashi gaiden and he had even less motive (and ability!) to fake his own death than the 4th did. Additionally, personality aside Obito is just as unlikely to fall in with a gang of criminals as the 4th would be. However, in a very recent chapter (357) a new piece of evidence arose that might not only overcome this argument, but even turn it backwards.
In 357, Sasuke attacks Tobi and cuts him down with a single blow. On the very next page, Tobi rises to his feet, completely unfazed by the attack and without even a drop of blood on him. Not even Hidan could boast such durability- he bled all over the place and rather than instant regeneration, simply treated his wounds as annoyances. There has only been one other instance of such regerative power in the series: that displayed by the reanimated 1st and 2nd Hokages in chapter 120, whose bodies simply drifted back together when damaged. This suggest the following:
What if Obito (and by the same token, the 4th Hokage) were reanimated using 'Summoning: Impure World Resurrection'?
At the start of the battle between the three hokage, Orochimaru erases the personalities of the 1st and 2nd Hokage. It is not such a stretch to theorize that, as well as ERASING personalities, the controller of the reanimated could REWRITE them as well, or the reanimated one's memories, especially if the controller were a ninja of the caliber found in Akatsuki. If we accept this theory as true for now, the question then becomes: who reanimated them? Although it COULD possibly have been done by Orochimaru, this is EXTREMELY unlikely. Orochimaru resented the 4th, as he had hoped to succeed the 3rd as the new hokage. Additionally, he would have maintained a level of control over the reanimated one even after rewriting the personality, which makes his subordinate position in Akatsuki and his subesquent decision to strike out on his own absurd. Even more notably, there is absolutely NO way in the world Orochimaru would have reanimated a one-eyed Uchiha brat who died years before in a small incident in a much larger war and who didn't even display incredible talent in the first place. However, the Impure World Resurrection was not a technique Orochimaru himself invented (like 'Living Corpse Reincarnation' was) and so could have been used by another ninja. But who?
THE FINAL MEMBER.
The final piece in the puzzle, the piece that ties everything together and makes it plausible, is the ninth member of Akatsuki. This member is the biggest secret in Naruto to date- they have not had so much as a single line of dialogue and have only been seen, through a blurred, projected image at Akatsuki meetings, a very small number of times. Surprisingly, there has been little to no speculation about this member's identity.
I am not going very far out on a limb by suggesting that this final member is a woman. She has a slender build, long light-blue hair (as seen, again, on the cover of chapter 317) and wears a flower in it (as an aside, she appears to be in her mid-20s). Additionally, the reason she hasn't spoken a word so far would be that, assuming she uses normal female speech patterns, it would immediately give away her real gender. Besides, given the number of kunoichi in the series it would be downright odd if Akatsuki didn't have at LEAST one among them. Virtually every ninja team has a kunoichi (Sakura, Tsunade, Hinata, Ino, Tenten, Temari, even Karin). Additionally, these kunoichi frequently have an inclination toward medical nijutsu. So it would not be such a stretch to imagine this final member as the medic-nin of Akatsuki (after all, SOMEONE had to reattach Deidara's arm). As a medic-nin, this member would be the most likely to know the Impure World Resurrection, whether by mastering it herself or learning it from Orochimaru (it may even be possible that Orochimaru himself learned/stole it from her during his time in Akatsuki). This kunoichi may even have sought out Orochimaru in order to learn the technique from him. This would make the most likely candidate for her village of origin to be Konoha, where she would be familiar with Orochimaru and his abilities. However, much has been made of keeping her identity secret up to this point, so her identity is most likely significant, possibly a character who has appeared before but is currently unaccounted for in the Naruto canon.
The next issue would be her motive for reviving the 4th and Obito. One possibility is that, in reality, this kunoichi is the REAL mind behind Akatsuki. As the Akatsuki members (with the exception of Zetsu the scout) travel in pairs, the kunoichi virtually MUST be travelling with the Akatsuki leader. It is possible that she revived the 4th because she needed his ability to use 'Dead Demon Consuming Seal', or rather, to develop it into the 'Sealing Technique: Illusionary Dragon Nine Consuming Seals' in order to execute Akatsuki's world domination plan and that she is manipulating him from behind. Although this is possible, I find it unlikely. For one thing, it's an absurd amount of effort to go to for such a plan to work and the plan just seems too much like it originated from the AL himself, rather than having been given to him. More importantly, it doesn't explain why Obito was revived. Although it's possible that the 4th requested the mysterious kunoichi revive him too, given his new personality I doubt he'd display such sentimentality. Indeed, the only possible reason anyone could have for reviving Obito would be personal.
So to recap: for this theory to be sound, the ninth member of Akatsuki would be a reasonably young kunoichi with incredible medical skill (able to detach and reattach a humans' body parts with ease), long, light-coloured hair, who may be from Konoha, is unaccounted for and has a personal reason for reviving not only the 4th Hokage, but also Uchiha Obito.