It's not from one of the classic Star Trek games then if that story was around, I've too pretty much had all the classics on hand; Armada (Omega and Timeship), Armada 2 (which was more 8472 and Transphasic Nebula, but REALLY bad gameplay because everything was weak as heck and it was impossible to control properly early on before later patches fixed the positioning issues due to the 2.5D design of the battlefield), Bridge Commander (The best, being able to fly into weapons fire to take the hit, whilst your allies rally around you and take out the offender is unmatched in any other game so far I'd say, also modded it a lot of it back in the day; made one of the better CGSovereign Hardpoints back then), and Star Trek Legacy (which was pants, as it had terrible modding abilities, as well as having a pizza box universe instead of a full 3D space like Bridge Commander), anything after that I don't remember dealing with the details of the Romulans, Nero and the Borg. So if there was such content, it wasn't in this list of classic Trek games.
No, it didn't sell well. It was also a very niche product, even back in the day. The biggest problem was that most people found that the "graphics" were not up to par compared to the stuff available in the other stuff. But then the modding community showed off what could have been with it for many years. NanoFx and high res models, with updated backgrounds made for spectactular screenshots. And then even other content from other franchises showed up and made it even more fun.
As for a proper Sequel to Bridge Commander, there was lots of projects that wanted to be BC2, but none have ever really got to the stage of release. Almost every one of them have fallen instead into becoming something else or was just a GoFund me project by the people behind the attempts. Really wished the original team wasn't disolved and given another go.