The Advanced Evolution Project is a corporation of many scientists working to advance the evolution of ponykind. They are the main antagonistic organization of The Eleven Day Rain and Cost of Destiny.
The Advanced Evolution Project was founded and controlled by Dr. Viktor Schleifen, and consists of a large body of brilliant scientists, working to further push the boundaries of genetic alteration to increase the evolutionary processes of different kinds of ponies to create a new breed of superior beings. Although, their cause does not justify their means. They commonly abduct and experiment on individuals they see as potential candidates for the project, born or unborn. Most subjects have not survived the process of genetic alteration. The AEP Headquarters is stationed in an incredibly secure and hidden location underground, and is sheathed in a protectiver barrier of nanoparticles that hides the facility from any means of detection.
The technology used by the AEP is extremely advanced, easily 100 years or more ahead of its time, as they have been free to experiment however they want without anyone interfering. They have been gaining enormous funds from an unknown source for their research, and in that have created hundreds of high tech devices. Their main and flagship technology, however, is their genetic alteration technology, allowing them to create superpony beings out of normal ponies. However, the process of perfecting this has been long and slow, and has resulted in the deaths of many hundreds of individuals.
The individual under the name Project Exile was simply an embryo when the AEP began genetic tampering. They continued experimenting off the research previously gathered from many other test subjects and eventually, 9 months later, the subject was born to a surrogate mother. The pegasus baby was put into a cryogenic chamber that supplied it with everything it needed to live and grow. Then came more alterations. Eventually, the baby grew into a full sized colt, and upon release from his chamber, it was deemed that he was, in fact, alive. This was the first successful prototype for the AEP, and was praised as the first herald of the new era. However, the protoype was unstable, and he went insane and broke out of the facility in a frenzy. The prototype was later discovered by Lightblade, who had engaged him in combat due to being attacked. The prototype had taken up the name Gravity X-Fold, after the gravitational properties of his powers.
After Project Exile escaped, the AEP decided that eventually, it would come back to them for answers. In the meantime, they worked off the data from Project Exile to create more successful prototypes that were stronger, faster, and more deadly, with a high diversity of abilities and traits.
Lightblade is a subject of extreme interest for the AEP. After they had discovered Light, they took immediate action to try to study him, and gave him the name Project Shard, due to his actual name being unknown to them at the time, although they could never get close enough to study in depth. They relied instead on detecting his powers when they skyrocketed, and relaying the data to their research facilities to try to replicate. Every attempt failed, but did bring about various weaker powers which they used to create their successful prototypes. In the eyes of the AEP, Lightblade is the master template to be used to create the perfect being, and advance the evolution of the pegasi, unicorns, alicorns, and earth ponies. The study of Light and Gravitz brought about the creation of the AEP's most powerful subject, Project Ramiel.
The AEP was brought to an end when Lightblade destroyed the facility's nuclear core, causing it to detonate and destroy the entire place, along with all remaining projects and all research. After this the AEP ceased to exist entirely.
The Advanced Evolution Project returned when the creation of Artificial Evolved became legal in countries outside Equestria (although it was a new organization as far as the public knew). This AEP has nothing to do with the old, and works as a private military company (PMC) that creates Artificial super soldiers for military use, or augments people with enough money. Due to this, Artificial Evolved bave been growing in number extremely quickly.