The Rainbow Factory was part of the Cloudsdale Weather Program, but even the rulers of Equestria were unaware of the monstrous activity that went on inside it's black walls. For pegusi were murdered for their color, which is used to create the beautiful rainbows.
One day the ponies inside were infected with a strange virus, created by the perished pegusi bodies. This caused the ponies to go crazier than they already were, and giving them extremely long life.
The Rainbow Factories employees now believed that they had to create rainbows at any cost, meaning they would take anypony from anywhere, whether they were pegusi, earth ponies, or unicorns. Even the four royal alicorns were at risk from the Rainbow Factory.
At first ponies just disappeared from streets, not leaving a lasting remark. But soon the Rainbow Factories ponies armies invading whole towns and cities. For the Rainbow Factory used half of the captured ponies to create rainbows, they turned the other half into their army.
The royal alicorns, then tried to stop an invasion of Ponyville ridding them of the virus. But the ponies in the Rainbow Factory were not so pleased. They built robotic suits around their army, preventing them from being subdued by magic.Soon, they had invaded Cloudsdale, Manehatten, Phillydalphia, and were ready to invade Canterlot.
When Canterlot was taken over, the Royal Pony Sisters were taken and murdered, to create another rainbow. At that point the Rainbow Factory ponies realized that needed a leader, and they knew just where to get one.
When they invaded Ponyville, a few ponies survived fleeing to the Crystal Empire, but most were not so lucky, for the Rainbow Factory had found it's leader. They took Rainbow Dash, and turned her into a monster. Rainbow Dash perished that day, leaving Rainbow the Destroyer.
With so few ponies left, Equestria was in ruins, leaving the Crystal Empire all that remains of civilization. In a desperate attempt to save the world, the survivors had one last plan to rid them of the Rainbow Factory for all eternity...
