Rainbow Dash arrived on the steps leading to the entrance of Twilight’s castle. Rainbow’s heart was beating three times as fast as normal, she had no clue what was happening, and WHY it was happening. She reached the castle doors and knocked vigorously. No answer. She knocked again, but this time she heard Twilight’s answer

“Go away, please! If you try to come in I will not be afraid to hurt you!”

Rainbow could hear the fear in Twilight’s voice. She was about to open her mouth and say that it was only them, but something stopped her. What if that threat was true? She knew that Twilight wouldn't hurt her friends, but from what she heard, she couldn't be sure. What she heard in Twilight’s voice wasn't just fear, it was hysteria and desperation. The last time that was put together was when King Sombra returned. It was clear that he had gone insane, and was desperate to retake the Crystal Empire. They had just barely managed to defeat him.

If Twilight was serious, she risked herself, or even worse, Scootaloo. She stood there for several seconds before saying

“Twilight! Listen, it's me and Scootaloo, nobody else! Could we come in?”

She stood there for what seemed like an hour. The frenzy on the streets had only gotten worse as numerous fires had start, all out of seemingly nowhere. There was one huge difference though, a distinct moaning sound could be heard from what seemed like everywhere. Finally the door opened. There stood Twilight and Fluttershy, Twilight’s horn was lit, and she stood in what looked like an attack stance, while Fluttershy held a long knife.

Rainbow Dash and Scootaloo were taken back by the sight, that was until Twi and Fluttershy’s stance fell with relief.

“Oh Rainbow Dash, you're alive!” Twilight said as she hugged her friend. Rainbow and Scootaloo then walked inside the castle, and the doors closed from behind. They were quickly boarded up by Twilight’s magic.

“Twilight what's going on? Why is this happening?” Rainbow questioned.

“Rainbow… remember when I went to Canterlot this morning and when I came back I was acting odd?”

Rainbow Dash simply replied with a nod.

“Well, Princess Celestia called me and Cadence there to talk about a new disease… Well diseases spreading through Equestria. The first one is a highly regenerative, parasite. It waits for the host to die before it takes place. Then this is the part we don't understand, the parasite reanimated the brainstem and cerebellum. Then it brings back the Ventromedial Nuclei, which tells you to eat. That means than any infected pony has only the need to eat, and for some reason we don't understand, they only eat meat…” Twilight stays quiet for a few seconds before continuing.

“When the infected pony bites somepony, they not only spread the parasite, but another disease as well. It's highly lethal, and from what we could tell, was a method to kill any pony that survives a bite. The first symptom is a very high fever, then followed by extreme pain from what feels like everywhere in your body, then you lose nearly all strength, then finally it's followed by coughing up blood…. Until your body gives up and you die. Then the parasite takes charge and the cycle starts again…” Twilight trailed off as she said that last word.

“When we were there, one of the lnfected that we were experimenting on, escaped and killed the guards. Those guards turned and started attacking the other ponies. Celestia and Luna told me and Cadence to go back to our kingdoms and to attempt to control the infection…. But I failed and now Ponyville is burning. She told us to keep quiet to prevent panic, but now that I think about it it would be best to have told everypony to wait inside their homes until this blows over.”

Rainbow Dash and Scootaloo stayed quiet for several minutes as they tried to process the information they had just received.

Rainbow Dash was about to break the silence, when Twilight spoke up. “The only way we know of to stop them, is to separate the brainstem from the rest of the brain. Either that or to damage it beyond compare. We've found that either blunt force trauma or impact magic works best.”

“Say that in English, Twilight!”

Twilight rolled her eyes before saying ‘'Basically you either hit their head hard enough to crush the brainstem, or use magic that will physically hit the head so hard it crushes or disconnects the brainstem.”

Rainbow Dash stood quiet, she realized the grim situation they were in.

“If it's that bad shouldn't we go and find Rarity, Pinkie and AppleJack?” Fluttershy spoke up rather confidently.

“Pinkie is dead, Fluttershy…” Rainbow Dash’s voice broke as she said that, she struggled to hold in her tears as she said that.

“Wait, what!?” Twilight stood shocked.

“We found her dead in Rarity’s shop..”

Everypony remained silent, all mourning the death of their beloved pink friend.

“I guess we should go then. I don't want to risk the others. Is everyone ready?” Twilight announced.

Everypony responded with a less than cordial “Yes.”

They all knew what they had to do, they would look around Ponyville for Rarity, and then once they found her, they would go to Sweet Apple Acres and pick up AppleJack and if they were still alive, AppleBloom, Big Macintosh and Granny Smith.

They gathered by the door to Twilight’s castle, mentally preparing themselves for what they needed to be prepared to do.

Twilight opened the door and they from there they galloped and flew, dodging the various infected ponies that they met.

The few that they couldn't dodge, Twilight blasted with her magic, killing them instantly. It hurt Twilight to know that she was practically killing her subjects and previous friends, but she had to. They were infected and were very much already dead.

AppleJack trotted along the path to Ponyville. She had heard a lot of commotion. She was just about to reach the main road, but then she saw somepony else..

Author's Note

I guess I have a slight explanation

My depiction on how the infection starts is (in my opinion) the most likely an actual zombie virus would come to be. The one thing I forgot to mention was about the frontal lobe, the frontal lobe basically controls rational thought and emotion. In this case, only the primal parts of the brain would be reanimated.