Just spotted this thread, so I'm transplanting my idea from the game ideas thread...
Idea number 1: Persona series/Firefly
The catastrophe at Miranda was the result of secret alliance tampering. The secret psychic experiments were done at the behest of the Alliance and the Blue Sun. Both were done in the interest of increasing order, peace, and control.
What's interesting is that neither of these disasters bore the hallmarks of politicians. They were too heavy-handed, too technological. Politicians work with words and people. They know how to be subtle, and how to control people by playing on their emotions. Miranda and the Academy didn't touch politics with a ten foot pole. No, these approaches bear the fingerprints of military officers who trust in weapons, soldiers and technology- not politics.
From this, and from the deep involvement of Blue Sun in the Academy, one could conclude that the Alliance is under heavy control or influence by the military industrial complex. Running off of that....
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There were two reasons for the Unification War- Ideology and Greed. The demand put on the Alliance by the war fed the growth of corporations who could feed those demands. The Alliance government thought that the corporations were solidly under their control. It was thought that no matter how strong Blue Sun and their competitors grew, they still had to listen to the government, and there were laws in place to keep them from gaining undue influence on the government.
As it was with so many other things, the Alliance wrong. By the end of the Unification war, a tight alliance of wealthy businessmen and influential generals held much of the real power. When they discovered the power of psychic abilities and the strength of Persona that lied underneath it, the military jumped at the chance. But their hopes at creating reliable, unthinkingly loyal weapons were doomed. To control and call forth one's Persona, one must face their own flaws, their own fears, and the lies they tell themselves. This requires thought. As the Shinjo group once proved, one can force a person's Persona to manifest without soul searching. However, this comes at a cost to sanity, health, and control. But the Alliance keeps trying, and while success is evasive they make progress. They branch out, testing the limits of Persona, poking at the very fabric of reality and mind and looking for ways to exploit it. Then a young doctor rescues the Academy's most powerful reader, threatening to expose their deeds.
Meanwhile, age old forces stir. Mankind is judged as sinful, and marked for destruction. Philemon, Lord of Persona and the better nature of mankind incarnate, argues for mankind to be preserved. This is a stage, he says. Humans have forgotten the lessons of their past, and the tragedies and horrors that a sinful few commit will teach humanity the dangers of arrogance and the lust for power and control.
Nyarlahotep, avatar of the worst in humanity, argues for mankind to be preserved. As an avatar of humanity, their destruction is his own. What he says is that to destroy mankind now is too hasty. As in his bet with Philemon ages before, the better nature of mankind is likely to triumph, even with the deck stacked against them.
Lucifer, leader of Chaos, argues for mankind to be preserved. Let he who is without sin cast the first stone, he says. Mankind's sins here stem from the desire for control, to force all others to submit to his will and live in peace. YWVH desired the same, as many of law followed him. Can we condemn man, he says, for a sin we have committed ourselves? Would it not be better to destroy only those who desire such control, instead of all human civilization?
YWVH, leader of Law, argues for Mankind to be preserved. Weakened and made less harsh over the years, he declares that it is not right judge mankind without a trial. One cannot be judged, he says, without a proper test. He points to Izanami, to Nyx, and to his own failures. If we do not make a test, he says, we will become the test, and pass or fail we suffer when mankind strikes against us in fear, rage, and desperation.
The beings of the demonworld sneer and call the four weaklings and fools. Caught up in dreams of remaking the mortal world, they set their plans into motion. Philemon, YWVH, Nyarlahotep, and Lucifer set thier own plans into motion, Plans to defend the Persona users awakened by demonic interference from Alliance and Blue Sun, and to unite them in the name of survival. And caught in these webs is a Firefly-class ship by the name of Serenity...