This is what happened, as best as we can piece together.
The object Qlippothic gave me was her galvanic tesseractor, set to explode - providing enough energy to catapult Darien back to a distant age, and presumably sever the Hydra from him in the process. How do I know this? What we thought was Darien's father, Jeremiah, was also Darien this whole time! How do I know this? I was able to possess the empty shell of "Jeremiah", which meant he was a Seventh Son and not the Sixth. (Despite Jeremiah's twisted experiments, NO scientific folly can outwit the Bloodwing Curse!) And this second Darien is the one Qli reanimated and restored with the memories of the first.
This means that the Darien we defeated survived the timeshift, and was fatelocked to find his way back to the Steam Age. After I exorcised the serpents from myself when Dr. Mason and I cured the the Baroness's twins, the Hydra seized a Dr. Mason as they were instructed, but not the Dr. Mason we knew! This timelost Darien then impostored as Jeremiah, kidnapped Sumalee and my sister Lumina, challenged his younger self to the haunted tea party, and eventually fell in combat to his doppleganger. And now, he has returned in a circuitous route to the exact point from when we banished him!
Now the question that haunts our family is, when did the Seventh Son take the guise of the Sixth? Some of you wonder if Jermiah and Darien were the same individual all along. I tell you with all certainty this is impossible. Yes, Jeremiah created his son Darien as a clone of himself, and the fact that he allowed Darien to develop his own identity as a scientific control against his other failed experiments made him a Seventh Son.
Qlippothic tells me that a clone cannot replicate itself infinitely. There is degradation, however slight, with each generation that leads to the eventual demise of the lifepattern. Therefore, Darien would not have cloned himself with the knowledge that his progeny would then do the same. The Knot of Fate would unravel.
So the switch had to have been made after the Darien we have all known was decanted. I am still investigating when this point may have been, reading the surviving records of the Foundation from the last generation and asking Darien what he remembers of his childhood. If only the memories of this Darien had not been erased! What a strange tale he would tell us!
Did this Darien perform inhuman experiments humans and nekos? Did he enslave the neko that would become the mother of his younger self's child? Every question leads to more and more difficult questions.