Some different ideas to add to the mix:
Beardy is Jovi: He is older in this story than he was depicted with Johanna in Rob's artwork. The younger guy with glasses is the younger him. Jovi has the power to give enhanced abilities in return for soul, and he is using this power to create warriors to resist the empire.
Empire: The empire has its own "god", Sara, and they are using her powers mixed with technology to create entirely soulless phantoms, more powerful than "natural" warriors. What does the God Machine really do? It extracts souls and stores them, turning it into a kind of living thing, and a mental bridge between Sara, who is controlled by the empire's leaders, and the phantoms themselves. The machine is furthermore mobile and is largely organic. Heck, who am I kidding, it's basically a techno dragon.
Rising: Jovi's strong gift enables him to manipulate the God Machine instead of being "eaten" by it. He interacts with the souls kept there and severs the bond to Sara and the empire's control. Merging with its latent sentience, he makes a sort of (temporary) peace with it, and with its powers he finishes off the battle.
Also, could Through the Looking Glass also be related? It does have a glimpse of story to it, but is also vague enough that the Phantom Shadow reference ("It fuels the fire in my eyes") could be anything from a beloved expression to a red herring. Either way, adding it to the imagined storyline gives an interesting angle to the ambition of Skye and the Renegades.
I can feel the sands of time
Passing through the hourglass
And it shimmers in my eyes
As I linger in the wake
As eternity escapes
I begin to realize.
We'll walk a thousand miles just to see for ourselves.
Look behind our eyes
Find our hell.
And in the light of the sun we go.
Through rain and raging snow
To find the things we do not know.
I will go
Never laying low
Just tell me how to breathe
And I will make it so.
You must know
That this is not for show
And if you are not wise (it will)
Be your demise.
Once I walked along a field
Another nightmare in my mind
And beheld the fearful symmetry.
Everything was beautiful
Even things that were dead
And I surged with violent imagery.
I walked a thousand miles just to see for myself
Looked behind my eyes
And found my hell.
We'll walk a thousand miles just to see for ourselves.
Look behind our eyes
Find our hell.
And in the light of the sun we go.
Through rain and raging snow
To find the things we do not know.
I will go
Never laying low
Just tell me how to breathe
And I will make it so.
You must know
That this is not for show
And if you are not wise (it will)
Be your demise.
We come to honor; to stand or die
To pass the hours of our lives.
We burn the silence and all the lies.
To fuel the fire inside our eyes
We all go!
And in the light of the sun we go.
Through rain and raging snow
To find the things we do not know.
I will go
Never laying low
Just tell me how to breathe
And I will make it so.
You must know
That this is not for show
And if you are not wise (it will)
Be your demise.
Come to honor
Stand or die.
Fuel that fire in your eyes.
