Laputa in this crossover being founded by a group of ponies who had broken away from the three tribes, during their search for a new land which would be known as Equestria later on. This group landed in a different part of the world and encountered an exceedingly rare magical element, Atherium (Volucite in the original Japanese version). They would base their magic around the properties of this crystalline element Developing independently and completely seperate from Equestria’s magic as well as making some breakthrough and inventions such as metallic Alicorn-like golems. Utilizing the antigravity nature of Atherium, these ponies would go on to the build a floating city. And thus, the Kingdom of Laputa was formed.
 
The kingdom enjoyed an Era of Peace, but that came to an end when a tyrannical king usurped the throne. He militarized the golems and developed a superweapon capable of wiping out an completely destroying a large area of land, known as the Thunder of Laputa.
 
Eventually, Laputa began to terrorize the fledgling Equestria and on several Occasions destroyed and layed waste to several Equestrian settlements with their armies of flying golems and the main superweapon. All in an attempt to subjugate Equestria as the Laputian ponies have grown vain and egotistical, Seeing themselves as gods, and everypony on the ground, their subordinates.
 
Eventually, Wizards from the Unicorns and Pegasi banded together to stop the Laputian Threat. They conjured a great and neverending storm around Laputa. Imprisoning the island and leaving the Laputian ponies in a bind until they perish from starvation and the hostile nature of the storm. Some tried to escape by fyling directly through the storm, but failed as dragons made of lightning would attack them and kill them. Only a few managed to escape. and are believed to have taken with them an Aetherium Necklace. Their only link to their long lost city.
 
With Laputa fully abandoned. The City is reclaimed by nature and over time becomes an overgrown ruin. The Great Tree, once cared for by the Laputian Earth ponies, grew to a tremendous size. spreading it’s canopy over the garden walls. Over the course of a thousand years, Laputa’s structure began to deteriorate. Both from exposure to the elements and the Tree’s roots pushing deeper into the entire structure. The lower level of the city had crumbled away, exposing the black dome within and resulting in one side of the castle completely eroding. Exposing what would otherwise be underground chambers and corridors. The only occupants left in the city are the Metal Golems. They either lay dormant, waiting to be reawakened or spend their entire existence, caring for the garden.
 
In the aftermath of Laputa’s imprisonment, Princess Celestia and Luna ordered that any record or trace of Laputa’s existence be destroyed and erased. The memory of Laputa fading into legend, and finally into myth and for a good reason. To ensure that Nopony would ever venture up their and get their hooves on the Castle’s weaponry and use them for malicious intent. For it will bring great Harm and Suffering to the People of Equestria and the entire planet.