Well done. I like how the Starfleet-Maquis tensions are still in play. Chakotay is ready to sacrifice himself to the Cardassians--but other than giving him a head start, Janeway is not ready to go the full nine yards to defend him
, even after his near sacrifice. That does fit with the rather Machiavellian captain I seem to remember from the series, and plays on the tension that I don't think was ever fully exploited the way it should have been on VOY.
In some ways this is more satisfying than "Endgame," though of course that means the rest of the series didn't happen. Not being a real VOY fan, I could accept this as canon.
While the Cardassians are shown simply as enemies here rather than anything more complex, I do like that you were true to canon--there was a statement once on DS9 about the Cardassians making their enemies chase sensor ghosts, which is very fitting to the way that ship followed Voyager. It also seems to me you followed Gul Jasad's embarrassment with the wormhole in "Emissary" with a demotion to a smaller vessel. That makes a lot of sense, especially since the conduct we saw from him in "Emissary" did not suggest someone with a lot of self control or the ability to rise up in the ranks--though granted, he does seem to have learned a little bit more about when to bargain rather than just be belligerent.
I wonder what the ramifications will be of getting that new propulsion technology. That could really upset the apple cart in some interesting ways during the Dominion War if it allowed both sides access to each other without the wormhole...