Phew, just got all caught up with this fascinating story.
Now while I'm not a huge fan of the more militaristic and authoritarian interpretation of the Star Trek universe, it is a clear testament to your skills as a writer that I got quickly swept up in the tale of Republic
and her hard-ass captain.
The premise is pretty darn good in itself even if perhaps not entirely original. Ship and crew fall into disgrace and the only way to safe the ship from complete dishonor is to bring in a captain who knows how to straighten out a crew which has all but given in to complacency and failure.
And Dahlgren clearly is the right man for the job. Only barely handicapped by his hopefully temporary disability, this is a man who would feel right at home on a Klingon ship, considering his penchant for total discipline, rousing speeches and blaring battle songs across the ship.
I thought the story is a bit long overall but that's not surprising considering that you've packed at least three, seemingly independent plots into one story. I suppose I would have expected those to be separated.
Those stories are compelling however. From the early training sessions and getting to know the crew, to an old-fashioned throw down with a TOS-era like super computer to the current story of the incoming generation-ship, kidnapping humans for their sinister purposes in best Mass Effect fashion.
And while those stories may have evoked others concepts, you've given them enough twists and details to make them your own.
My only real critique at this point may be your character's tendencies to explain themselves and narrate events and often give surprisingly detailed orders. While this really creates a sense that Dahlgren is a sly old dog who knows exactly what he's doing, sometimes it feels as if it slows the story down unnecessarily with yet another speech or another plethora of orders.
I sense that this may be inherent to your writing style however and of course there is nothing fundamentally wrong with that.
Overall this this is an impressive Star Trek fanfic and the rate at which you seemed to have crafted this is quite mind-blowing. Yeah, I might be little jealous at your prolificacy there.