I am extremely bored so f*ck it I'm posting my shower thoughts to get them out of my head.
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In the beginning there was the pure world where the talented became gemstones and the rest were out of luck, but at some point they discovered magic, essentially a bug in the system, and distorted the world beyond repair, creating imagine breaker in the process as a last ditch contingency.
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Around 100 years before the main story Aleister receives visions from Aiwass (a being from the pure world) and later lays the foundation for academy city via the Abbey of Thelema and creates the first artificial esper around 40 years later. Using magic, specifically his own new religion of Thelema, he corrects fate by awakening the powers of those who had their growth "stunted" by the world. Wether or not he's aware of that doesn't really matter.
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Around 16 years before the main story Kamijou Touma, Accelerator, and Hamazura Shiage are born around the same time.
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Around 10 years before the main story imagine breaker accidentally creates/births Kazakiri Hyouka (a production line for Aiwass and an anti-magic weapon).
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In the main story our protagonists get involved in the magic side, face progressively stronger enemies at shorter and shorter intervals. Science somehow manages to keep up with magic despite the glaring power gap and advances at an ever growing pace (the clonoth, fuse=kazakiri etc.).
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The distortion of the 4 elements gets fixed, the magic gods lose most of their power, special right hands pop out of nowhere, the science side makes its own world Tree to "kill" a major demon, and whatever it is that hides inside imagine breaker grows in power.
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The magic side is becoming unstable at an increasing rate with no real signs of stopping.
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Now my theory: the pure world was distorted to the point where the people intended to be espers did not awaken their powers, and that fate has been trying to correct itself the entire time. With Aleisters esper program and it's consequences serving as the largest breakthrough to that goal yet. Essentially Fate is using magic to destroy magic.
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Edit: maybe that's Aleister is the 4th hero? I just re-read this whole thing and he sounds more and more like an unwilling prophet, which make his motivations even more hilarious. No matter what he's really never free.