Scrapped Princess/WMG

Pacifica Casull is God.
As the only one unaffected by the Peacemakers' mass-brainwashing powers (that not even an uber-swordsman like Shannon could resist), she has to exhibit some power a level or two higher than Lords Browning and Mauser, even though she doesn't like to fight.
 * Higher? Mauser was the Peacemakers' boss; she (and presumably Browning) had them well outclassed. Pacifica's abilities stemmed from, and as I think they explained in the show itself, that's why she was able to resist the brainwashing.
 * For that matter, you could probably make a decent argument for Mauser herself, not least that she already has a church devoted to her... (Granted, if so, she's not much of a capital-g God, but it's anime, what else is new.)
 * Given the resemblances, I figured it's closer to Pacifica being a clone of Celia Mauser. Peacemakers aren't authorized to affect her let alone killer, and she can break their effect, though not completely order them. Not that she tried. If she was just anti-brainwashing genetic engineering I'd think they could blast her, unless Celia was stopping them. Which she might have been... wasn't the clearest ending I've seen.

Chris was on Pacifica's side from the beginning.
Even during his battle with Shannon in episode 4, he never seems to be deliberately aiming to kill him. One possible reason for this is that fighting inside the cave would do harm to Winia, who at this point had been part of Pacifica's party until Chris had taken her as a hostage. Since he had no one to fight for as a knight until that point, he chose instead to defend Winia, one of Pacifica and Shannon's new friends.
 * Considering Chris was shown to possess the Guardian gene, appearing on the screen in the fortress with Winia, Shannon, Raquel, Leo, etc., he's genetically predisposed to being on her side before he even meets her. So technically, this is canon.
 * Except he also was with those who Zephiris said did NOT have the gene.
 * She's referring to his subordinates.

Pacifica couldn't be harmed by the Peacemakers because of her resemblance to Mauser.
There's a distinct resemblance, and the Peacemakers were originally the Valkyries, programmed to obey Mauser. The resemblance is probably good enough that it triggers a safety override in the Peacemakers, intended to protect their master. Browning knew of this, and programmed it into the design of the Providence Breaker, so that the Peacemakers would be unable to destroy her.

Towards the end of the war, some humans almost created a spell with a feedback loop which would destroy Earth
Which would be well foreshadowed if this show ever had a prequel.

The final days of the war were fought After the End
This would explain how all the ruins came about. Perhaps more importantly it would also explain why the war was only fought by about four or five people in the end.

The guardian gene enhances natural ability
Thus why Shannon and Raquel are pretty much the strongest and most capable characters in their respective fields. This wasn't stated outright, but is nonetheless likely true.

The aliens exist on a higher plane than humans
Again, never outright stated, but we never see an alien, and they are made out to be much more enlightened than humans, who are said to be unable to understand their true place in the universe.

Pacifica still possesses powers that could bend or strip back reality
Thus, allowing humanity to ascend to a higher plane of existence.