I just watched Star Trek: First Contact again, and then I reflected back on Voyager. What's going on there? Are the Borg gone? Is the Queen finally dead, or is she forever lurking?
There are only a handful of major Star Trek stories that have taken place after the the last episode of Voyager (Endgame):
- Star Trek: Nemesis - No Borg
- Star Trek: Countdown - This was a canon comic book mini-series published as a lead-in to the 2009 Star Trek reboot. It takes place in 2387, 9 years after Endgame. In it, you see the supernovas endangering Romulan Empire and the efforts of Spock to use the red matter to help solve the problem. In particular, the Romulans enhance the Nerada (Nero's ship) with Borg technology, implying that, at the least, some Borg technology remained functional even after the deployment of the neurolytic pathogen.
- Star Trek Online - This MMORPG takes place in the prime timeline in 2409, 22 years after the destruction of Romulus. One of several storylines is the Borg reappearing after more than 30 years of quiet post-Endgame.
So how you answer the question depends on how you interpret the canonicity of Countdown and Online.