So we know now that Izanagi is the father of Tsukiyomi, Amaterasu and Susanoo. And as we all know, Itachi used Tsukiyomi and Amaterasu from his left and right eye, as stated in the myth. The only thing that Itachi didn't do is to release Susanoo from his nose; this doesn't make sense anyway since Mangekyou abilities are Doujutsu abilities
Now, how is that all retated to the Manga, and above all, the incidents of Itachi's appearance?
Itachi mentioned something very important, as shown here: Chapter 386, Page 09
Itachi said that there is a 4th Mangekyou technique; it might only be achieved if the User has EMS or the MS. This 4th technique would be Izanagi, since he's the closest to Tsukiyomi, Amaterasu and Susanoo.
Itachi himself hinted he knows most about his master: Chapter 385, Page 17
He referred to Madara as "invincible immortal". Noticed how his glare was in the top-right panel? It was more a concern, a sign of hatred than a praise. It would make sense that Itachi is the one to help defeating Madara and learned the secret of the Mangekyou since he was Madara's apprentice. This again would mean that Itachi's help in the upcoming war is inevitable.
One way to gain the EMS is to pluck the eyes of someone who already uses the MS. However, as Kakashi already prove with the MS, there might be another way to gain the EMS than already shown.
However, there's one problem in this entire theory: Itachi died, unfortunately. But Zetsu said something very suspicious; at least in my opinion: Chapter 394, Page 06
He mentioned that Itachi actually never showed off his true power; If you think about it, Zetsu was right about that. Itachi never was serious against anyone, not even in his final battle where he was supposed to be serious and show everything that he got. However, Zetsu's statement is quite foreshadowing for this theory and for the future of the plot. Itachi never showed off his true power, ergo he must be hiding something; something that we've never seen so far.
As I explained in another theory, Itachi gave his soul to both Naruto and Sasuke. So he could have survived due to that.
Final part, what is "Izanagi" capable of? We all don't know yet, since this Jutsu has never been introduced in the Manga. We can only assume what it's capable of.
Many people assumed that Sasuke used Tsukiyomi at Danzou: Chapter 477, Page 16
Well, this most likely isn't the case. When Sasuke used Tsukiyomi on Bee and Shii, the form of the Mangekyou didn't change at all; In fact it remained all the same. However, this isn't the case in chapter 477. The form of Sasuke's Mangekyou did change in a weird way; It covers almost his whole eye.
This might be a proof that this is indeed Itachi's doing and not Sasuke's.
In chapter 385, there was a side note that referred to the Mangekyou as "Mirror of Thousand Flowers". When the change to Sasuke's Mangekyou form happened, it changed more in the form of a flower and the shape looked a bit like Itachi's caleidoscope.
We've never seen that kind of form before; This is neither Tsukiyomi nor Amaterasu. This is Izanagi, the 4th Mangekyou technique.
If this is indeed Izanagi, Itachi obviously used it to emerge out of Sasuke. This would also explain why he has his MS activated. Danzou is shocked for good reason: Because this is no Genjutsu, this is indeed Itachi.
People predict that Izanagi might also be the way Madara survived so long; The body Madara has obviously isn't his own, because Itachi said that Madara is just a mere shadow of himself. The Izanagi technique probably helped him to transfer himself inside a body; The prediction also states that if the owner of the body is full of darkness and evil, the person who used Izanagi will take over and the owner will cease to exist.
Itachi doesn't want to kill Sasuke in this way, that's why he probably split his soul and didn't give it entirely to Sasuke because Itachi knew Sasuke would choose the wrong path; That's why he also said to Naruto "but I hope you never have to use it." Sasuke has already fallen into the darkness; That's why Itachi took over Sasuke's body at half. And that's also why he wasn't surprised when he turned into crows. Crows have also been used in a Non-Genjutsu context earlier.
Probably Sasuke won't know that Itachi took over his body, thus he will continue his revenge until he encounters Naruto.
