I am not normally a fan of fan fiction. I think that most of it is crap, especially the stuff I've written. But this is really, really, really, really
well done. The characters are engaging, there's a real sense of mystery and suspense, and I'm not getting the sense that the story is just assembled from a collection of preexisting Star Trek plot devices. I also really love how the technology is depicted in a realistic, grounded, non-magical manner.
My only quibble is with the character of Polly. I'll come right out and say it-she's a Mary Sue character. She's incredibly attractive and intelligent with a list of accomplishments more suited to someone three times her age. Everyone wants to sleep with her, or be her best friend, or both. My teenage self would think she's a bit over-the-top, and he once wrote a Star Trek/Star Wars crossover that featured his very own Mary Sue character-a 16-year-old Starfleet lieutentant-getting Jedi training from Yoda before having a lightsaber fight with his evil Mirror Universe doppelganger.
But still, even though Polly stretches believability to its breaking point, I am still enjoying the heck out of this story and eagerly look forward to more. Fantastic job!