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Long before the Great Autobot-Decepticon Civil War, there was a female scientist working in the protoforms nursery. She was just an average white collar doing basic maintenace. However, she was fascinated about how the protoforms came to be. Those protoforms who will become Cybertronian citizens. She wanted to be more involved in the creation process so she started studying. However, she barely finished some studies when the bombs rained down on the factory, killing everyone but leaving the poor fembot badly damaged.
That war was an abobination. No way she'll take either side, both being as horrible as the next. So, she remained a pure Cybertronian.
Years, centuries, millenia of pointless conflicts between the Autobots and Decepticons laid waste to Cybertron. All the while, the Protoform Scientist repaired and heavily modified her body. And she studied. She experimented. She stated modifying some protoform to see if it would make something greater than a Bot or Con. It failed horribly. Still, she DID somehow created life. So, she named herself MOTHER, forgetting her old name. Learning from her mistakes, she worked even harder and did many experiments. She now had two more sons. Both had a mission. To go to both warring factions to be her eyes and hears. Both invented themselves a character to play and went away. One to the Autobots, one to the Decepticons. Her sons relayed precious intel for her research.
When the war went to Earth and other organic planets, this gave Mother so many ideas. Some dangerous ideas. Ideas that would change Cybertron forever and maybe, just maybe, put an end to this senseless conflict.
