And if I'm not mistaken, by the time this event took place, the Romulans had allied with the Federation and Klingons after that messiness with Senator Vreenak, so I was also looking for some closure after the fact, to see if there was later mention in any of the books. Clearly this adventure didn't wreck the war effort.
I'm not sure what their methodology was, but according to a chronological list of Trek episodes I have, "Message in a Bottle" took place a little while before "Pale Moonlight," around the same time as "Waltz."
So that helps.
There was an SNW story that showed the Romulans actually hijacking the
Prometheus (or maybe it was in Tales of the Dominion War? I'm pretty sure it was SNW), but that's all I remember talking about it.
Strange New Worlds V, the aptly named "Who Cries for Prometheus?". Like the episode, it states quite clearly that the Romulans aren't involved with the Dominion War (i.e. it's during the nonagression pact period). The episode aired almost three months before "In the Pale Moonlight".
I just re-read the story, and my takeaway is that the Romulans are acting quite boldly, probably knowing that the Federation can't retaliate harshly (the Dominion War and all that) and certainly in desparate preparation should the War shift against them and they have to defend themselves against the Federation and/or Dominion.
I like to imagine that part of the deal bringing the Romulans into alliance with the Federation was probably to wipe the slate clean for the attempted hijack and slaughter of the 50 Prometheus crew members. Of course, Rekar and his Tal Shiar compatriots were all taken into Federation custody, so most likely the Romulan Empire disavowed his "rebel group" and that was that.
As for how the hijacking took place: We aren't really shown it firsthand in "Who Cries for Prometheus?" (which takes place in Sickbay, at first). What the story reveals is that it happens very quickly, and appears to start from the Romulans somehow beaming onto the bridge, slaughtering the bridge crew as they alert the rest of the ship, and within a matter of seconds, slaughtering all but six of the Prometheus crew. The Romulans, of course, are aided by their own sensor readings in hunting down the Starfleet crew, and our three heroes (Ethan, Nancy, and Stephen) take to hiding their biosigns with some sort of super-secret concoction ("Facade Three") to evade the Romulans throughout the story.
But none of them make it out alive. The character Stephen is killed when he attempted to send out a message to a nearby alien array (hmm...) and Ethan is the dying officer that the Doctor meets at the end of the story and in "Message in a Bottle".
