It's 5 years after the Pony Wars between the Pegasi, Unicorns, and Earth Ponies. All the ponies are happy and are living in harmony, but unknown to them that a vicious evil was about to be released on ponykind as a new unicorn had been born. This unicorn had been born with a disease that's now known in modern Equestria as 'The Pony Plague.'
It is very rare and can only be introduced through genetics. This disease is so rare that it only appears in about one of every one trillion ponies. Along with that, only couples of either Pegasi and Unicorns, Earth Ponies and Pegasi, or Unicorns and Earth Ponies can have a young filly that is born with it. On top of all that, about one in ten of those couples would have a filly who contracted the disease so in all actuality there is only a one in ten trillion chance that a pony would contract the disease, to put it bluntly, it is very, very, very rare and hard to get.
The unicorn had been born with this devastating disease and it quickly spread to the mother mare, since the disease is so contagious. The symptoms of 'The Pony Plague' on the horse like creatures of Equestria are that first the mane gets really, really frizzy. Next, their eyes dilate as the three white spots on their pupils fade, along with very powerful migraines. Lastly, their cutie mark, if they have one, shrinks until it is almost unseeable to the naked eye. Once all that happens, 'The Pony Plague' spreads throughout the ponies system, putting them into a deep coma, from which the pony only has a slight chance to wake from the coma.
'The Pony Plague' had spread through this old time Ponyville to almost all hundred of the members of the town in just six hours. A stallion messanger from another town had come to deliver a package, and when he left he had the disease, but he hadn't suffered any symptoms. He walked back to his town, infecting every living creature he passed by including, but not limited to, Minotaurs, Ponies, Griffons, and Dragons. This had been a mistake as this made the disease quickly spread all throughout Equestria...
In modern day Equestria, this 'Pony Plague,' now thought to be impossible to ever return,had been reintroduced by an Earth Pony. The worst part of this disease to is that it even effects Alicorns, this meant that Celestia and Cadence had gotten it too, and it even got Chrysalis and the now friendly Discord.
Twilight had been visiting Ponyville as part of her new life as an Alicorn Princess. She had arrived to make sure everypony was okay, but most of the ponies weren't very well off, all of them with quarentine signs hanging outside their doors and windows. When she arrived she saw a pony collapse in the middle of the street and Twilight had rushed over to her.
"Oh my gosh! Are you okay?" She asked, very worried, but all she got in return was a cough from the weakening pony. Twilight thought that now she was infected, but she was more concerned with the populous than her own well being. A few hours later she arrived back at Canterlot Castle and didn't have a single symptom of the disease. Curious, she pulled out a few books for an answer.
"Hmm, there's got to be a reason why I am not getting ill..." She trailed off into her book. She had searched through the books and eventually got to one of her family tree. It turned out that her family has a rare gene that will resist this disease, it only came around in one of ten ponies in her family, and she had it! She read through another book about when the disease had come around the first time...
As old Equestria had been ravaged by this disease, Twilight's ancestors, Brightmoon Sparkle, who had the very first cutie mark to represent 'magic,' he was a tall stallion unicorn who was a shade whiter than Shining Armor with an all white mane and a five o'clock shadow, and his wife Darksun Graywing, who had a dark yellow mane with a streak of red and a streak of orange in it, black fur, huge gray wings about as big as Celestia's wings, and a cutie mark of a pegasus, unicorn, and earth pony holding hands to represent friendship, as she was really good at helping ponies make friends. They both had the resistance to this disease. Luckily Brightmoon had been a very skilled caster and had devised a plan to cure all of Equestria of this disease. The problem was that the spell required either a healthy unicorn to give their powers up willingly, or a pegasus to give up their wings willingly.
"I will do it." Said Darksun, smiling with a loving look in her eyes, holding one of Brightmoon's hooves with both of hers.
"No, I can't let you do this!" He replied sternly, putting his hoof down.
"Please let me, you are the one casting the spell, and I'm the only healthy pegasi left in all of Equestria!" She said, putting her head against Brightmoon's chest. He hesitated for a moment and finally said,
"Okay honey, if you want to, I guess I will let you..." He said as he wanted to tell her 'no'.
"Thank you Bright, I will be back in a bit, I love you." She said as she flew off to execute the next part of their plan. She had placed some crystals in very precise spots and returned to Brightmoon.
"Okay, they're in place, I'm ready." She said as she stood their waiting. Brightmoon had hesitated for a bit and then cast the spell. Darksun's wings had started to fade as the spell Brightmoon cast had hit a crystal and then the beam of light that was the spell had travelled to all the other crystals, breaking up and making a huge chain effect which had cured every single creature infected with the disease, even the ones in a coma already...
"Wow, my ancestor gave up her wings so she could save Equestria? What an awesome pony!" Twilight giglled as she remembered the problem at hand. She had started flying around and she used her magic to bring giant crystals from the Crystal Empire to specific landmarks and major cities around Equestria. As she placed the final crystal, she remembered that there were no healthy Pegasi or Unicorns left, she was the only one in all of Equestria who had this disease resistance. Then Twilight got an idea, she had one shot at it, but she decided she would give up her wings to save Equestria, just like Darksun had done before her.
"Alright I have one shot at this, FOR EQUESTRIA!!!" She yelled as she cast the spell, but something was wrong, her wings weren't disappearing, the whole land had been doused in a huge flash of light, and... it stopped. Everypony had been cured, but at a cost, all the ponies in Ponyville had seen Twilight laying on the ground unconsious, she was now an earth pony.
"TWILIGHT!!!" Yelled Rarity, Rainbow Dash, Fluttershy, Pinkie Pie, and Applejack as the ran to her side, completely ignoring the migraines they all still had. Twilight's eyes had started to crack open as she weakly said, "G-girls? Y-your all okay." Before fainting again.
Twilight had woken up in the town infirmary with at least half of the town watching her sadly.
"HEY! She's waking up!" Exclaimed Rainbow Dash, the first to notice her eyes crack open.
"What happened?" Twilight asked, rubbing her head while she tried getting up. She noticed her horn was gone and in a panick she demanded what had happened.
"You saved Equestria of course!" said Celestia, stepping in from the crowd. "You gave up your powers to save all of the land, even look at your flank." She said, Twilight looked at her flank and noticed she no longer had a cutie mark. Celestia smiled at her and gave her a glass full of some sort of juice.
"What is this princess?"
"Drink it and you'll see!" She smiled again as Twilight had drank the whole cup's worth of the liquid in one gulp. Just then, her eyes started to glow as she was lifted into the air and her head and flank started to hurt. After a few seconds everypony in the room noticed her head started to sprout a horn and her flank grew her old cutie mark.
She had floated back down to the bed as she noticed she was a unicorn again.
"Princess, but how?"
"Just think of it as a get well gift, from Zecora." She smiled again.
Mayor Mane had walked into the room and smiled at Twilight as she said, "Twilight Sparkle, thank you very much from us to you, as a token of my gratitude, I had Pinkie put a party together for you!"
"Wow, thank you Mayor, I'm just glad everypony is safe." She laughed and everypony lived happily until the next threat of evil would come to sic itself upon Equestria.