And, moreover, the EOS fighters, the ONLY enemies you fight in the final stage, are all unmanned. Also, the end of the war happened shortly after Hyperion's destruction, as both sides were no longer able to fight...
And how could you advance in rank AFTER your death? Moreover, WHY were YOU chosen, instead of some random Sodom troops?
So here's what I think REALLY HAPPENED: Sometime during the first six stages, something happened in Hyperion's strategic computer that caused it to become self-aware (whether it was because of a program error, a computer virus, or something that the developers of Hyperion didn't foresee, I don't know). Hyperion decided that machines are far superior to humans, and decided to assert that by trying to wipe out all military forces. So what Hyperion REALLY meant at the end of stage six is: "All mankind shall know that machines are their rulers when I annihilate the armies of both Selene and Sodom...starting with you." But Hyperion's strategic computer, made for only military purposes, prevented it from saying just that, which led the protagonist to believe that Selene had turned against them. I bet that, during the year between stages six and seven, Hyperion used the EOS fighters to attack both Selene AND Sodom. (Chances are that Hyperion issued similar messages to all other Selene pilots before it destroyed them.) And the manned Selene aircraft that the protagonist DID shoot down? They were just trying to flee from the EOS fighters. If they managed to survive the EOS fighters...they would just get shot down by the protagonist. The protagonist never realized the real truth: Hyperion had turned against Selene, while still considering Sodom an enemy...and in doing so, it had become the enemy of all mankind.
So in the final stage, you actually aren't rebelling against Selene...you are rebelling against Hyperion, showing it that humanity REFUSES to be the slaves of machines. Hyperion, in the midst of its desires to prove that machines are superior, forgot one thing: Humans can destroy machines just as easily as they can create them. And as you know, Hyperion remembered this the hard way.
And one last thing..."But the name of the one who indirectly brought about the end of the war was completely erased from the official records of both powers." How much do you want to believe that, just before Hyperion's destruction, it sent a transmission to both sides requesting exactly this?
