Drakengard 2 but Manah is the protagonist and we actually feel chased like terrorists for opposing the Knights of the Seal

The Knights of the Seal slaughter almost the whole Resistance. Manah desperately at the verge of death after being captured and tortured to tell where the remnants of the Resistance are, is trying to escape as she finds a Black Dragon imprisoned and almost dying too

She makes a pact with him and the price is that she would never feel any trace of happiness again

This causes a change in her personality, she becomes ever less faithful of the future, questioning if it wouldn't be best for the world to disappear. She also has distorted flashbacks of her mother yelling at her and beating her

She wakes up hearing screams, screams of those who died thanks to her, screams of the Goddess, who agonizes in pain, screams of younger self
She starts going insane with those screams, but Legna helps her keep at least part of her sanity

I'm just giving some random ideas that I have, should I continue?

Eris is pretty much the same, but she actually works for the Knights for her own pride, and despises Manah because she poses a threat to the Knights but also because she envies Manah for having a goal of her own and being free
Eris would be a recurring boss maybe even End.A boss

Their rivalry would kinda mirror Zero and One's rivalry

Ahem* We get to kill Seere

And we have to see Golem trying cease Seere's pain while they both slowly die