The Imperium's fall was a dawn of a new age for the warp's most powerful inhabitants, The Chaos Gods stirred and laughed with glee and joy at the fall and death of their Anathema, the human worlds are now lost without the Astronomicon, the guiding light shut out for millions of years, yet still, lifeforms thrived against chaos.
The humans built small empires that spanned far too small to be considered even a galactic empire and so, many of them risen out of the ashes and fell into the well of life, and so did many xenos species that now, without the imperium, began rising out of the ashes of humaniity to dominate the stars.
Chaos has been an ever-growing cancer tumour effecting the galaxy like a plague that spreads across the souls and minds of the many species across the galaxy. Even though they have grown so vastly powerful that they are nearly completely self-sustaining, without a food source fixed, they began to dwindle in power and soon, fond themselves dwindled back into powers very low, which allowed the weakening of Slaanesh's grip on the Eldar souls.
Khorne's bright and fiery realm began to dimm, Tzeentch's castle winded and begun to make a little bit more sense, Nurgle's many poxes within his garden started to dissappear and Slaanesh;s grip on the many souls she was entitled to consume begun to slip. The last event mentioned was something that caught the attention of many Eldar, Exodite, Craftworlder and Drukkhari alike, the Eldar cult Ynnari, while sustaining many casualties, was able to steal the last Cronesword from within the palace of the prince.
Ynnead, the Eldar God of Death was born in not a flash of blinding light but with a cold dark void that seemed to expand and caused a large disturbance within the immaterium.
Ynnead, now awwoken, did battle with the Dark God, and finally, after years of suffering by the Eldar, he was able to defeat Slaanesh, with only a small shard of it escaping into the warp below, freeing the Eldar of the sisn of their ancestors. The death of Slaanesh was a true saving grace for the Eldar as they ebgun to build their empire once more.
It was found that it was not the gellar fields that protected the Spacers living within their asteroids or transport, but rather, the power of worship to the Emperor ove rthe course of many millenia, was able to form a puddle of a small God wiithin the immaterium that shielded the asteroid-dwelling humans until they were able to develop technology to shield themselves manually. These Spacers would try to reach out to the Eldar, however, after what they have done to the many human population of many empires that rose from the ashes of the Imperium, contact was not an option.
The scars of the War in Heaven inflicted upon the Immaterium , after a few million years, were starting to heal overtime, with Ynnead overseeing the reconstruction of the Eldar Gods and holding off the now miniscule forces of Chaos.
However, it would not stay that way for very long, the Necrons attacked with their forces and killed many species during the Cleansing, tainting many parts of the Warp once more as Ynnead, now is unable to stop the rising power of Chaos, due to the many rampant emotions of dying species. They grew and grew to heights even stronger than Horus Heresy and soon, overwhelmed by the Chaos Gods. The Eldar, horrified at Ynnead's defeat, blamed and waged war on the Necrons, and launched the Haven War. The many Avaatars of Kahine reforged and fused their souls, and thus, a sliver of Khaine's power manifested in the immaterium. Soon, the Eldar lost and were subjugated, the Necrons's found a new power source revealed by the Laughing God, Slaanesh, thus, the Necrons began experimenting and torturing the Eldar, molding and modying them into twisted and painful abominations, the Eldar turned to mindless subjects to power not just Slaanesh, but Khorne, Nurgle and Tzeentch as well. They risen to power never seen by a warp god before, and continued to rise for the next 40 million years.
Isha, looked on, horrified at what they were doing to her children, screamed and begged for Nurgle to stop the suffering, the pain of the Eldar, but, it was no use as Nurgle only smiled and moved on. Isha's mind began fracturing and tearing itself apart, piece by piece, until it reached a breaking point, she tore apart her own soul and soon, she awoke, her emotions seemed to have pulnged into the void. Nurgle, now very concerned, checked and tried to talk iwth her, but n answer was found, no matter what he did to her.
Khaine, in response to the Blood God powering, also ebgan taking in the suffering of the Eldar, he ahted it, he hated how guilty it made him feel, after eons, he began to mature due to the consumption of not war, but the uneding torture fo the Eldar, he now sees the world in a different perspective and has seemingly been humbled over the years.
Soon, the War In Heaven Secundus was launched, and after 70 million years of war, the Chaos Gods and many entities residing in the immaterium grew so utterly powerful that reality began to tear itself apart, as entire regions of space began to resemble closer to the Warp. The Subjects were taken and put in incubation pods on star-sized mega-structures stored in the fortified Eldar webway until the war was over under the watchful eye of the legions of Tau Earth Castes and Cegorach. There they sat, some who are intelligent were plucked into the digital world such as the Processors.
The galaxy was completely devastated by the War in Heaven Secundus, with only a few thousand systems left in the galaxy and the galactic center, the galaxy was empty, for the conditions were too hostile for any life to develop anywhere within the galaxy. The Asteromorphs and Tau launched "The Great Rebuilding", where they began to rebuild the galaxy once more. To do this, they must clean the immaterium first of it's taint and create billions of systems to repopulate the galaxy once more, and they know eactly the two for the job.
Khaine within the warp was completely dwarfed by the Gods, he hid and soon, the Asteromorphs approached him and offered a deal, what the deal was would be interpreted differently across all the Eldar Cultures but what it truly was would most likely remain a mystery. Khaine accepted and was given unimaginable power by the Asteromorphs, he was now no longer the Eldar God of War, no longer the violent berserker of the Eldar Gods, now, he was now Khaine, the Destroyer of Gods, he would bring light back to the immaterium, nothing more and nothing less.
The Asteromorphs were able to liberate the cold dead God that was once Isha and introduced her to the Colourfall, a compacted well fo Eldar emotions that the Asteromorphs were able to scoop up before their enslavement to the Necrons, Iisha dranl it and felt emotions once more. The Asteromorphs offered her a deal, go to the materium and create new star systems and repopulate the galaxy, in return, they would provide ehr with the well, deny, and she would have nothing. what she chose was very much obvious. She would not be known as the Goddess of Fertility and Harvest, she was now Isha, the Creator and she would bring a new age of prosperity for her children and many more.
Isha and Khaine's progress throughout both realms exceeded expectations, with millions of systems produced and large swans of the warp cleaned within a thousand years.
Khaine was stubborn and hot-headed, he held no patience or care for disgusting warp vermin, and soon, the Chaos Gods were deafeated and toppled voer by khaine's furious might, the Immaterium was filled with the sound of the screaming and wailing of many entities, until it stopped. In a million years, the Chaos Gods and the countless warp entities have been permanently deleted by Khaine.
The Immaterium had returned back to it's natural form before the original War in Heaven, a sea of souls and non-hostile entities harboured the new Immaterium, with Khaine's humble home sitting somewhere inside.
Isha proceeded to not only restore the galaxy, but extend it and soon, it became a supergiant galaxy, nearly 20 times bigger than the original, nearly all have potential to harbor new and unique forms of life. However, something was wrong with Isha. Due to having no soul, she no longer can care for her children or any species and only viewed them as characters in stories, now only seemng to care about her own desire: To create new systems, seemingly psychotic in nature to many who truly know the Creator.
Khaine, now alerted, went to confront Isha and soon, the fight between Creation and Destruction has occured, thousands of systems were created and destroyed in the span of the 50 000 years. Soon, a truce between the two was erected, Isha would no longer create and Khaine would no longer destroy within the materium. Soon, Khaine retreated back into the warp while Isha led the Tau Terrestrials guided the Eldar while the reborn Emperor of Mankind led the Human Terrestrials guided the humans.
This was, unfortuntately, the last we have ever heard of them, it was known that through the belief of an unbelievable number of Eldar belief, isha was able to regain her soul back and the Eldar Gods resurfaced. The Transcendant Eldar say that they have moved on to a higher dimension with the Asteromorphs, however, there is evidence to suggest they were killed by the Asteromorphs after they lost their uses, what happened to them will remain untold for many generations to come.
(I didn't know the direction where to take Isha and Khaine so I just went "Ink and Error")