A little thing that popped into my mind during the final section (SPOILERS)

[DarkinBladeGaming]

Mother computer says that Ava (And presumable someone else due to it being plural) broke into the Phoenix vault and made off with Gail and Kitt. What I'm wondering is, HOW IN GODS NAME DID THEY DO THIS. Ava was a peace minister, armed with at best Thomas level tech. How did she get all the way through the Forbidden lands, into S.P.H.E.R.E, through E.D.E.N, Past Mother Computer, steal 2 children, and then get out alive, and all the way back to Panselo. There has been no evidence of Phoenixes anywhere other than E.D.E.N, so she couldn't have stolen them from one of the Vaults near the Archive or the one in Atai. Plus, to even get though E.D.E.N Gail needed the Sepheralis, which ava obviously didn't have. So what's up with this? She can't be an Alien or Phoenix, since She confirms that Gails Nana is her mother, so those two are out the window. Is this related to the Sinister undertones of the Peace ministers that the game hinted at? I'm honestly puzzled

[John Stellarum]

It could be part of the "sinister undertones" you mentioned. I'm inclined to believe that there are multiple causes to this, and that it's entirely possible that Ava and/or whoever it was that was working with her at the time is a metahuman, possessing the lineage of one or more Phoenixes who "slipped through the cracks", as mentioned in one of the logs in E.D.E.N. (I think it's one in the hidden room in Final Rest.)