So stood the divine alicorn sisters in one another's embrace. Tears streaming down one another's muzzles. Long feuds were forgotten and erased. Yet explanations were needed by the younger Princess of night. As their breathing slowed and their tears began to cease both Celestia and Luna separated and gazed into one another's eyes. Luna looked at her sister and spoke first her voice mellow and soft "Tia, what happened? Are all our subjects gone and dead? Why are you devoid of regalia? What is going on?" She asked her voice barely a whisper on the last question.
Celestia stood for a moment and then breathed in deeply listening to the soft breeze and the birds singing in the distance "What do you already know Luna?" She asked her younger sibling.
Luna spoke with a confused voice that sought clarity "All I know is I came down from the moon and everywhere I looked all ponies are dead. Whole families decayed and left to rot. I visited a large library with the remains of a Twilight Sparkle and Sunset Shimmer as well as a young dragon named Spike. I found their notes regarding something called bacteria or heaven's wrath. I visited outlying homes and farms and found papers with finely made images and information detailing the spread of this disease. Is no one left alive sister?" Luna finished her voice trembling and unsure.
Celestia looked down upon her younger sibling and spoke "You are correct regarding the major part of the story. I'm sorry you had to find two of my former students. I could not bear to enter the library and for the first few years after all the main events I could not even find time to live but mourned and lived as though it were a waking death. I've only just begun to heal and move on from all that's happened." Celestia swallowed hard and continued " The disease came from an asteroid that impacted some 5 years ago. Our astronomy team in Canterlot took samples and had them in containment. It was found during their initial investigation that the asteroid had this disease within it. We did not realize how dangerous it was until things were too late. Its own impact spread the disease high into the air and from there it somehow used magic itself to grow and evolve into ever more dangerous strains."
Sorrow filled Celestia's eyes and she took a moment to calm herself and begin again "By the time we realized the disease had been spread all across Equis and the world at large it was too late. Ponies, Griffions, Zebras, Dragons, or any other intelligent being fell victim to it. We attempted quarantines but the speed at which it could develop and change overwhelmed us. Somehow our world's magic and the magic in others permitted it to alter itself and any time we seemed to make advances in combating it through medicine or healing spells it found a new way to evade and spread. We closed down trade routes, we shut the borders, we blockaded ports but ever on and on it spread. Till there was nothing left." Celestia finished.
Luna looked at her sister in horror and asked "Nothing is left!?" said in barely a whisper. Celestia looked at the ground tears filling her eyes nodding and spoke "Nothing save myself, you, and Candance who is an alicorn like you or myself given divinity by harmony itself. All others are gone and past" Celestia answered.
Luna in terror spoke anew " What of Discord? Tirek? Others? There must be somepony! Anypony!"
Celestia answered the terror with calmness " When it became apparent what was happening we broke Discord out of stone in hopes his chaos magic could be of use. We were losing tens of thousands every week at that point. He understood the issue and was himself horrified. Our hopes in the use of Discord's magic had the opposite effect as it warped the disease once again and caused the spread even faster affecting even Discord himself killing him nearly outright. I personally removed Tirek and explained the situation to him hoping that if he might remove ponies magic and magic itself it might halt the disease. It was a last-ditch effort and it even worked for a week or two until Tirek himself also fell. With his fall the magic returned all across the land and it all began again. Our best estimates were the world population of various intelligent species was somewhere around 1 billion and it took less than two years for everything to end. I had to watch as pony after pony and friend after friend was lost. In the end, ponies and others across the world either simply waited for their own demise or worked against the clock trying to find a way to prevent the disease from going on. It was all to no avail." Celestia finished with fresh tears in her eyes.
Luna rushed to embrace her sister and whispered in her ear " What of you and of us and this Cadance? Are we yet in danger?" Celestia shook her head " Both I and Cadance never became ill for whatever reason. We think it may have to do with our Alicorn physiology but we were never able to determine why. We can scan for the disease and find it but it appears that it has burned itself out. I teleported all non-sterile samples, as well as the asteroid itself, and any remnants I could find into the sun itself. It was the last thing I could do."
Luna sank sat down upon the ground and shook her head as if it couldn't be true. Celestia simply kept up the embrace the older sister seeking to comfort her younger sibling but being unable to do anything to stem the flow of tears. There they sat till it was nearly time to lower the Sun and raise the moon.
"Come Luna. Let us go home" Celestia spoke lowering her Sun and raising the moon and stars. So Luna and Celestia arose flying in the cool evening air. Neither spoke more their attitudes sober as cold hard stone. They flew some distance away a journey of some twenty or thirty minutes and landed. In the bright moonlight, Luna could see a simple dwelling place made from sod, wooden beams/poles, with open windows that had oiled paper instead of glass. A simple chimney arose from the top. The primitive nature of the home struck Luna as odd as her sister had always had a flair for elegance.
Celestia looked on her younger sibling and answered as if reading her mind "After everything that had happened it didn't seem right to to me to live in luxury. I failed as a ruler and thus I don't find myself worthy of such things though Cadance disagrees. She should be asleep right now but you can see her in the morning." Celestia said.
Luna nodded her head, her mind and heart numb from the revelations. She entered and came into a large room with glowing embers in a stone hearth, a sink to to opposing side, and a very large bed frame fashioned from what appeared to be strong oak. She peeked under and saw the bed frame was made from interlocking ropes and the mattress fashioned and filled with straw. Where she had been expecting new and modern things she found things somewhat more familiar. In the bed, the covers moved up and down with somepony slowly breathing.
Celestia looked on her younger sister lovingly and closed the door securing it with a large wooden drawbar and went and closed each window. Celestia gently pulled the covers back and got into the bed the pony in the bed moving "Hush Cadance. Luna my sister is here as I said she was before I departed" Celestia whispered the pink pony nodding and choosing to go to sleep. "Come sister. Let us rest and tomorrow we can talk more and do what needs doing" Celestia said inviting Luna to get into the bed and under the covers with her memories of earlier times of their youth coming into both Luna's and Celestia's minds.
Luna simply nodded and removed what regalia she had left and got into bed with her sister. Celestia used her magic to snuff out the candles in the room and pulled her young sister close who had begun to tremble. Celestia began a lullaby and her horn lit with a sleeping spell and Luna's eyes closed gently. Celestia sighed and closed her own eyes their breathing moving in synch with one another. Luna's ear upon her sister's chest listening to her heart and breath. Night and day united with love all under the same roof. None of them really knew what might yet occur.