In the game and nothing seems to have changed!

[Arcell]

Whoa that's cool, having the final boss return to life before the end? Guess this confirms he'll still be alive in 2.0. Makes sense after all Atomos and it's actions haven't been explained and Yoshi-P said the current Umbra storyline would continue into 2.0 with explanations on the "truth" of the current events in future dungeons.

Also...are there...TWO Darnus's there? Now that's just mean....

There were at least 3, I heard there were more. If you want to tie it into lore then they could be clones created by Dalamud or something. Probably not actually part of the lore though.