Very inventive, very original. Given the quantum nature of time travel (according to some theories), Nathaniel might have already changed the past and redirected his own 'present' onto a parallel branching track, one where what went before won't happen again in the original track. Maybe the solution will come (assuming this situation is ever resolved) from the future Nathaniel has created, the one where the Kent descendants aren't caught in a dystopian nightmare where Tempus rules, in spirit if not in fact.
The technology of his captors is a bit scary. They command a Kryptonite-like energy analogous to electricity which they use to control supers. And if they have so much control, why are they still interrogating Nathaniel? Is there a Kent-inspired resistance to the overlord(s)? Was he part of a resistance cell which gave itself up to send him to the past to warn Clark and Lois?
Or is their analysis flawed, and the only force which can win the people's freedom the Kent descendants? Was he trying to stop the very events which would eventually break the tyrants' chains and release the oppressed?
There are so many ways you could take this that I can't list them all. I add my vote to that of the others: Let us see more of this story! The start is just too good to let it be a one-shot. Let's all bang our silverware on the dinner table and chant in unison More! More! More!
Pretty please, with pink Jello icing and strawberries on top?
