The demon emperor had many secrets, big and small, but there was one secret that was even more important than Requiem Zero.
He had the Apple of Eden.

At some point in his history, Lelouch found the Apple of Eden (I don't know how yet, but didn't take it from his father for sure)
He was not a Templar or an Assassin, although he knew about these factions and their infinite war.

In past, Charles was a templar but his "vision" didn`t combined with "vision" of templars or assassin`s so when he became the emperor, he and one of his wives(which was assassin)(certanly NOT Marianna) decided to destroy both factions.

Lelouch found a way to use the Apple to achieving his goals (gentle effect on the mind of people so that they stop hating each other and focused hatred only on him), culminating in Requiem Zero.

Of all the people only he and C.C. could use it but for different reasons: C.C. because her code synergized with the Apple, and Lelouch was able to resist the power of the Apple because ... well, he already wanted to take over the world and he had a strong will, something like that.

Only two people knew about the apple besides him: C.C. and Gottwald, Suzaku had no idea.

Deciding that the Apple was too dangerous for anyone to know about it, he decided to hide it.
And for this he created several vaults all over the planet in which it may lie, but nowhere indicated in which one. Also in each vault was one Masyaf key with Lelouch's recorded memories, only the most important, among which: Obtaining Geass, Killing Yufi, captivity by the Emperor and creation of Julius Kingsley, killing the Emperor and Marianne, Requiem.

One of the discs contains the dialogue of C.C. and Lelouch:
-Are you sure there is no other way? With Geass, you won't encounter big problems on the way, but with an Apple no one is even close to being able to stop you or even slow down.
- Sure. Even if you are right and I want to rule with Geass or Apple, what will happen next? If I die, what will happen to the apple? If someone finds it and wants to use it for their own purposes?

- Don't you use it for your purposes?

- Yes, it is, but I am well aware of its danger and that it is not just that the Templars and Assassins with their infinite war for the right to possess it.

-So you want to hide it so no one can find it?

- Yes, it is too dangerous for our world, even the power of Geass cannot be compared with the power of the Apple and therefore it must be hidden from the whole world in a place where no one will find it

-Correct me if I wrong, but creation of vault in the capital doesn't seems like a place where no one will find it

- Yes...Well you already know that this will not be that simple

-True...looks like you've already made up your mind...

-That's right, everything will continue as I planned. Let's go, there are other things we need to do.

A few years (2-5 approximately) after the Requiem, the Templars will contact his friends (Kallen, Cornelia,
Black Knights (further - acquaintances)) and tell them about the Apple and what Lelouch used it to enslave the world and convince them that the apple needs to be found (they will say it's for the good of the world but in fact they want it for themselves).

In the course of their search, they will find answers to the questions that tormented them all after the Requiem. In the latest vault,
where "absolutely" should be an apple, they will not find it, but recorded appeal in which Lelouch explains what an apple is, what he used it for, who the assassins and templars are, what each of the factions wants and warns do not search for the Apple because it will not lead to anything good. Maybe make a scene where he answers questions like in the scene with Mao or Schneizel (using the Apple, he found out what they would say exactly and wrote down the answer to it)

WARNING! Further will be an absolute nonsense that can only be invented under the Acid trip

1) light Acid trip

When С.С. found out that Shamna was looking for other pieces of Eden, she took the apple and decided to use it together with the World of C in order to bring Lelouch back from the dead. When С.С. brought Lelouch back, in the last moment acquaintances tried to stop her and something went wrong and in the end Lelouch absorbed the power of an apple and became almost a God (Let's make Mary Sue character even more Mary Sue)))

Then follows the events of the full-length movie, adjusted for Shamna's main goal of taking possession of other pieces of Eden in the course of which must necessarily be Lelouch's use of his new power against Shamna's army (simply because it's cool))
At the end Lelouch and C.C. find a new goal for themselves, namely the search for all the pieces of Eden.

2) Max Acid trip

In last vault acquaintances find a skeleton of Lelouch with Masyaf key (just like in AC:Revelations) in which repeats scene from Revelations adjusted for the fact that instead of the son of Altair there will be Gottwald and С.С.
With help of Apple Lelouch created illusion of him when Suzaky kill him, but illusion was with defect, specifically all damage dealt to the illusion is instantly and completely transferred to the creator. There will be an Apple in the vault and when someone touches him, a beam of light will fly out of him into the skeleton, which will return Lelouch to life. After that will be a short dialogue when Lelouch said that because of their curiosity he was back to life and all people that he killed when he was an emperor was for this moment to "charge" Apple so he can be brought back. After that with help of Apple he will escape with teleportation, find somewhere staff of Eden from AC brotherhood, then meet with C.C. After few weeks(month) acquaintances somehow find out where Lelouch hiding and go there just to find out that Lelouch(in their opinion) lost his mind and become a cultist. In truth he create a pentagram to summon Dream of the endless(A.K.A. Sandman) and make a bargain. Acquaintances if forsed to watch over this. First Sandman quite angry about fact that he was "Summoned like a little demon" but then he become interested in this deal.

Lelouch asks Dream to create a passage to another world(reality) for him and C.C. in exchange for staff with Apple and Spear of Leonidas. When Sandman ask why he should be interested in this deal Lelouch said that he knows about Isu and that they thought that they are stronger than the Endless, started war with them, shamefully lost and try to hide from Endlees. When Sandman said that this in not enough lelouch propose location of ALL piece of Eden in ALL realities.
Sandman agreed to this terms and create a passage(that looks just like portal to mirror dimension from Doctor Strange) and Lelouch with C.C. leave Earth. That`s all.