Cosmos takes Fluttershy’s words to heart. and pulls out all the hidden power that were buried deep in her genes.  
Time to rewrite history.
 
And so Cosmos looked deep into herself, and saw the missed potential in all of her past lives. Through her mind swam all the actions she had comited before becoming whole, and she scoffed at them. Her true past selves would never have acted in such a goodie-to-shoes way. And luckily they did not have had too. For as much good that they had committed there has always been the potential for evil.
 
Through her genes she was conected to the past in a way she had never been before. Cosmos had never had such a profound connection to the past. but now that she had. she was gonna exploit it for all it was worth and then some.
 
Like tendrils. Her chaos seeped back through time. Cosmos had never corrupted retroactively before. But now that she found she could, she was giving it her full attention.
 
The thought of all this shaos filled her mind with extacy. She had always been a Chaos goddes of the here and now. Creating chaos in the precent witour worrying about the past.  
She had not considered she could destroy not just the ponies as they had been in the present. But all that they had ever been. She would erase and pervert the very root of their beings, the very memory and history would be her playthings to reshape and rewrite as she saw fit.
 
As her genes traveled further and further back through time. History was being progressively rewritten, erased and renew. Replaced by a new cosmic truth. The truth that there was nothing but chaos in the uncaring universe. And from this truth emerged a new world in which all creatures had done away with morals and societal restraints, and embraced madness. A world where people were free to kill and maim and pervert unhindered. Free from the shackles of logic and reason.
 
It was a world in which Twilight sparkle had never been any ponies friend. Nor had her parents, or grand parents. The entire Sparkle line was bred for the single purpose of breeding the most powerfull unicorn in the world. A divine purpose bestowed uppon them by the tyrranical twis sisters
 
(Cosmos though they had been sisters at least - and by her divine will, they were.)
 
The very same sisters that had torn equestria apart with their bickering. Their civil war had destroyed and split the country, but none had destroyed the other, none had been sent to the moon, for as much as they hated each other, they knew they needed each other, as they were both destined to one day become one in the reborn form of Cosmos.
 
As was Twilight sparkle. and for this purpose she was sent to ponyville, to studdy the stars and find the shards that held her divine essence. To prepare for the coming of Cosmos, to which she had been bred to offer up her body and power. This was her destiny, as sure as the stars has been embedded on her flank.
 
 
As history was being re-written Cosmos form took on new elements to reflect the new times. Her mane. Which had previously been a miasma of protoplasmic beauty, bearing colors unseen on this planet, now gave way to a new element, where colors went to die. The element of Cosmic hellfire. Burning as bright as her beloved sun. Dark fire, As deep and cold as her beloved night sky. Not merely a representation of the stars above. But a burning tear in reality. Where the fabric of the physical was ignited, and the infinite depths of space shone through.