Freya uses a Naganadel. When Nihilego appears in WLL, I vaguely remember Cella saying that they appeared everywhere during the Calamity, so it's highly likely that they're related. Considering the nature of Ultra Beasts, it's possible they're from some sort of Ultra Space, but I'm not entirely sure. Maybe Kieran and Freya where actually present during the calamity?
I know that Freya did cause the nuclear meltdown in the Miera Region, and is somehow still alive despite her body being identified, though its possible it was the work of her illusions. Had Freya never done that, nobody would've found Aevium, which leads to the main story. I think Freya and Kieran are working to put events on a certain path, a "predetermined" path, and maybe fulfill the Light Prophecy considering Freya wanted to create Aelita, a possible Light... As for where they came from, the future sounds plausible, but honestly it could be anywhere because we have no idea where their technology came from. For all we know they could be Garufans sent into the future, or even people from an offshoot timeline who got their hands on some snazzy stuff.
One thing I've noticed is that what happened during the Calamity seems to line up with the Dark Prophecy: "The land shall shift, and innocent beings shall fall between the crevices". However, I don't think there were any of the four shadows during that time, and along with Vivian's spell maybe it's the reason Aevium is still standing.