I wrote a version and then changed my mind. After going through old lyrics and adding more detail to my imagined storyline, here's one of the possibilities I end up with:
Backstory: Our world degenerates into a petty war where criminals thrive. An evil empire is rising, and fighting them are ninja warriors. In time, the empire wins and kills or enslaves some of these warriors, while some escape. Their leader remains and keeps fighting in subtler ways. The empire then sets about suppressing the people, turning many into grotesque warriors (phantoms, part machine) through several experiments that subdue the mind and drain their souls. Experiments go wrong, and the armies run wild and kill all in their sight, threatening the survival of mankind. To stop them, a God Machine is being built; a mind-controlling satellite and a weapon with the power to scorch the Earth ("Five billion souls incinerated in the doom of the gods"). The Empire wishes to use it to restore order and fulfil their original plan ("the voice of God is everywhere / Now the terror is the other we / and their unholy deity").
Skye (blonde protagonist) and bearded man: she was the greatest of the enhanced warriors, until she was captured by the empire and made to do their bidding. After a long time, the ninja leader (bearded man) finds her and saves her, actually giving her back her soul. In her shock and confusion, she tries to make sense of how to do his bidding, but slowly she is finding a cause and an identity of her own. He actually wants to destroy the world and let it start anew from scratch, purer, more good.
Jovi (redhead), Pearl (RFID-cheek) & Perfect Dark: I'm going to guess this is Jovi and
JohannaPearl. She is another of the ex-ninjas, captured and forced through some of the trials of becoming a phantom. Never succumbing, she eventually escaped and restored her will but not all of her mind. As the phantoms attack her, a ninja hero (Perfect Dark) appears and saves her. Now, this guy is truly crazy, a "chosen one", powerful but insane, and he seeks to use both of them and the God Machine to kill everyone and everything ("bring the fall, the End of All"). He is instead killed by "our" two heroes, a transformative event for Jovi and for their relationship.
Agnes Cecilia (starface) and Sara: Several years ago, starface failed in keeping the phantoms from stealing away her little sister. Presumed dead, Sara is instead turned into a phantom.
Renegades and their leader: Maybe there truly was a grand design by the ninja leader, but he has become a megalomaniac and his decrees are not truth, only opinion. Another voice is the renegades, a pack of criminals who find themselves the lesser evil in the changed world. They value freedom and companionship, and the blonde chick joins with them. Several of the other ninjas of her past have already done so. In their company, she finds meaning and purpose, and a cause for her anger and hatred. She finds a powerful ally in their leader, a psychopath and murderer like her. (I can't find a better fit for the leader than the guy with the glasses on the left of the cover, though I don't like that match.)
Battle: They head for the headquarters of the empire, or what remains of it, to stop the God Machine. They meet the ninjas and team up with them despite their differences, as the phantoms close in. Infiltrating the fortress (on Snake Mountain), many of the warriors face their personal struggles. Sara appears and Starface has to defeat her. The blonde chick has chosen the renegades' side, not the "good guys' side" as her previous master would have it. She shoves her past devotion in his face, but he is proud of her.
Rising: Jovi becomes the first hubnester, by joining his mind with the God Machine, thereby changing its original purpose. Everybody else is dead, and the phantoms are still closing in. He will scorch them all in the hubnester's inferno and end the Empire's metal forged dominion. ("We'd place the light of our sentience within the machine / and we would send it to heaven to end God's regime") He will eventually be the first in a long line of protectors that will turn into a legend in the ages to come. ("in its celestial path in the sky / the great hubnester lies / The Legend of hubnesters fight will be told forever (JP)")