A long time ago, before Equestria was founded, three Ancient Artifacts were made by human scientists. These three scientists: Dr. Dash, WarCry, and Pinkamena created the stones out of anger, and hatred.
They infused themselves with the stones they made, planning to get rid of the lab, and the lab only.
When WarCry fused with her stone, called the Strength Stone, her body remained, somehow, the same in appearance. She spotted a two-handed battle axe, and picked it up with one, like it was a pencil to write with.
Pinkamena fused with her stone, named the Method Stone, glared at a piece of equipment, and it turned to nothing but scrap metal. The pressure in the air obeyed every look and gesture.
Dr. Dash, when she fused with hers; the Color Stone-felt her left arm, from mid-bicep down, turn painlessly mechanical. The runes had the words 'Pegasus Device' in Hebrew inscribed in the metal. A wire ran from her elbow, up the back of her neck, and into the base of her skull. When she touched a desk with her left hand, the runes ignited, and took the color from it, turning the object to ash.
When the three scientists were found, the wipeout of humanity began. By the time they were done, Dr. Dash, WarCry, and Pinkamena hated themselves for what they did, and hid for centuries.
Now, a millennium later, the human seven are given a task of teaching the three human scientists about the Magic of Friendship, while building trust with them.
Disclaimer: I do not own the characters of MLP:FiM, or MLP:EqG. I only own the fan-made characters.