Great story. This is the first I've replied to this thread since I'm new (relatively speaking; I started coming here once 'Through the Looking Glass' stopped updating.) However, I can assure you that I would have replied if I knew this existed.
It always amazes me how Buffy can be put in so many other universes and still fit. Authors for other shows don't even seem to try (I try to picture Charmed or Smallville in uber, even just contemporary, and I get a headache). I am a Star Trek fan (Though not hard core; I started with Xindi-Enterprise and have seen maybe half of each of the other series, though not TOS, through re-runs) This is one fic where I enjoy reading the comments to get references.
I have to tell you that I knew the Old Man was Willow's old captain ever since his first memory of meeting her. It's probably because I started 'Equilibration' on Sunday so it's fresh in my mind. Still, I didn't see anybody else rereading it to get hints.
Hopefully I won't have to wait another year for an update.