Okay so I originally posted this in Lemons mega thread but I feel like it needs a thread of it own. So we'll leave it there, enjoy the read and lets discuss.
Something, which we need to talk about, which I don't know if we have but here goes anyway.
Cortana's reincarnation. I could explain it, but I found a page which does it a lot better then I can.
http://www.haloarchive.com/the-library/the-reincarnation-of-cortana/Now here are some key parts I've taken.
The Flood were labeled as“Inferi redivivus” by the Forerunners which translates to “The Dead Reincarnated“. While the reincarnation method employed isn’t the same as an Overmind’s it is similar. By way of a Gravemind the Flood can pull up the exact consciousness of anything it has infected or directly control those already infected. In Halo 2 we see that the Gravemind has infected Regret and enthralled him though dominance didn’t need to be established at the moment while in Halo 3 the Gravemind speaks directly through Truth who showed no signs of infection.
This is the floods form, of choosing their consciousness, in a whole it is many minds, but it might somehow choose one to be dominant.
Now
While we haven’t seen an entire consciousness reincarnated it is in the Flood capabilities and a small example lies within Evolutions short story “Human Weakness“.
And then something brushed against her face, almost like the touch of fingertips, and she found herself turning even though she didn‘t need to in order to see behind her. It was that forest she couldn‘t identify again. The picture didn‘t reach her via her imaging systems, but had formed somewhere in her memory—and that memory wasn’t hers . She was seeing something from within the Gravemind. Behind it, like stacked misted frames stretching into infinity, there was a fascinating glimpse of a world she had never imagined, a genuinely alien world. Knowledge, so much knowledge. . .
―There, the Gravemind said. ―Would you not like to know . . . more?”
Cortana found herself standing in a pool of dappled light in a perfectly realistic forest clearing. She was still conscious of the sensor inputs into the mainframe that housed her, but the temperature and air pressure matched her database on climate parameters for deciduous forest. She still couldn‘t identify the trees, though. She‘d never seen them anywhere else. The name of this place . . . it matters little except to those who love the knowing of it, the Gravemind said, fading up from a mosaic of pixels in front of her. He resolved into a solid mound of flesh, superimposed on the tree trunks. Beyond the alien forest, Cortana saw exotically alien buildings in the distance. ―So many have been consumed. Such a waste of existence to be devoured and forgotten, but what is remembered and known . . . becomes eternal
[Quick summary of “Human Weakness“] The story takes place as Cortana is still on high Charity with the Gravemind after Halo 2 up until John rescues her in Halo 3. In this time the Gravemind constantly interacts with Cortana’s systems to such a degree she isn’t aware of what is her own doing or it’s what are her thoughts or memories. The excerpt above is a scenario in which the Gravemind brought up the memories of a being it infected and projected those images into Cortana’s “mind”.
This is basically the Gravemind, well melding itself with Cortana, giving her memories of those it has consumed, and in turn gaining her knowledge, whilst planting its own. From here you can see where I'm going, well maybe.
Now, did anyone watch Halo Legends: Origins Part 2? Do you remember this scene?
Halo Legends was shunned by the Halo fanbase in unison due to the overwhelming artistic liberties taking with character designs and events. Soon enough the Theorist circle started to noticed we may be witnessing future events within Halo Origins, such as UNSC and Covenant forces working together to prevent the Flood from spreading and A RETURN TO THE ARK. What has eluded us all from high to low is a certain scene in particular.
Now I'll explain this return to the Ark theory, which to my understanding, is the Chief returning to the Ark in search of answers, why? what? could be a few things, to defeating the Flood entirely (we never did get to know Cortana's solution to the Flood) or maybe a way to bring her back.
Now assuming Chief reading the Terminals in Halo 3 is canon, he did have contact with something, that made its way back to the Ark, a Forerunner AI, Mendicant Bias
“And so here at the end of my life, I do once again betray a former master. The path ahead is fraught with peril. But I will do all I can to keep it stable - keep you safe. I'm not so foolish to think this will absolve me of my sins. One life hardly balances billions. But I would have my masters know that I have changed. And you shall be my example.”
This is what Chief is told, now a small fragment of this AI which was set on the Covenant Dreadnought (the Pyramid thing) and was helping the Covenant (the AI also started the Human-Covenant war accidentally by telling the Prophets their holy relics were actually meant for humans, and basically starting a religious war)
So getting connected back to the Ark made Bias come to his senses (he was in rampancy, oh thats convenient), now the rest of Bias was buried by the IsoDidact under sand on the Ark.
Now with this, what happened to come out of a large content of sand?
Watch it, watch it again. First, doesnt the surroundings look like the Ark? 1:57 looks like the waterfalls on the Ark seen in Halo 3 (and that multiplayer map)
Secondly, he looks up at the Machine, then Cortanas chip, Bias escaped rampancy, maybe he could know more? This could be Chief going back in Halo 5.
Back to Cortana
Now, in Halo 3 the Gravemind, was defeated on High Charity, and sought to rebuild it self on installation 04 (the Halo being built by the Ark) which it also failed, meaning the Gravemind, has a telepathic Hivemind to a certain range, obviously a Gravemind is needed to control the Flood, and they all know the same knowledge, now we don't know if they all present the same persona, but lets say one doesnt. Lets say one, took on the personality of an AI, it got to know very well, an AI, that got to know it, very...very well.
What if, the Gravemind, is the reincarnated Persona of Cortana, the Ark wasn't destroyed completely, so whose to say all the Flood died? Whose to say what people thought was Cortanas solution, failed, and just halted the spread for now, as the main Gravemind was on 04, which was destroyed.
Whose to say Flood didnt remain on the rest of the Ark? The Novel 'Hunters in the Dark' showed to us that the Ark was still there, heavily damaged but there.
Now, I should have put this further up, but here, for reference.
Here is my theory; A Gravemind was cut off by some means and-while still serving the Flood- grew to act of its own will by whatever degree. If that isn’t a likely scenario then perhaps Cortana is instrumental in stopping a threat to Chief and the Flood. Or maybe The Flood is no longer being controlled by vindictive [transsentient]Precursors,… By whatever means or reason a Gravemind grew in singular and saw fit to reincarnate Cortana for Chief. Silentium showed how the Gravemind reconstructed Mendicant Bias once the Infection spread. Could a reincarnation of Cortana be so far-fetched with what were presented with in Origins? Her return may not happen in Halo 5 but something of the sort might happen later on.
The search for Cortana, lead to Bias, the Flood threat is still there....the solution...the Gravemind, Cortana somehow having an influence in the Gravemind to surface....possibly this was her solution, to rampancy, to the threat....of the Flood.
Cortana could split forms of herself in Halo 4 due to her rampancy, that begun on High Charity, whose to say one wasn't split and seeped into the minds of the Gravemind, the presence....and in turn become a Gravemind....her solution to stop the Flood, was perhaps, to control it? Like Mendicant Bias so long ago...but Peacefully...or at least, in little hostility.
As the Gravemind in Origins, doesnt appear to be hostile, and hands Chief, a chip...Cortanas chip. Chief, having found Cortana resurfaced, hands the chip to the Gravemind...perhaps with hoping, to have his friend back. Only to have the Gravemind, give it back, tenderly place it back in his hands, as a memento, of the times they spent, but ultimately she cannot go back. This is what she must do. This also comes from Frankie, stating that Origins, may not be just symbolic, but possibly events that are yet to occur.
That friends, could be it. A word from Mendicant Bias, this comes form the IRIS saga, written by Frankie, to promote Halo 3.
You asked me once, what happened to those who vanished?
You asked me, why did we survive where our fathers fell?
You wished to know how we ever let it happen
A scourge that consumed the galaxy
And the cure that was worse than the cancer
You asked me once about my intent
And the spot that would not wash out
I promise you the answers lie in the Ark
Find me there in the dark
For that is where I abide 
