You know something struck me as a spin off idea of some of the material you guys are churning out...
What would happen if a Borg cube came into the Federation, then was ALMOST defeated, but it did something quite unexpected.. A parting mission, much like the Borg sphere in First contact, separated, and flew off, before anyone could catch it.. somewhere nearby... but then what would happen if all of the long range communications systems in the Federation started winking out.. Instead of infecting the humans, they infected the computer network! The immediate effect would be the Borg would have all access to almost everything in the Federation, and Everyone in the Federation would be completely cut off. Ships on deep space missions might not even notice at first, and colonies and species as much as 5000 Lightyears away might take months to fully appreciate what was going on - the Federation is huge and it relies on it's communications network to exist!
Rather than being a complete 'Armageddon' scenario, it would be more sinister, and scary.. Suddenly the fleet doesn't know where anyone else is, unless they are in long range sensor range, but they can't communicate. Something keeps infecting the comms systems. No one knows where the Borg are operating from.. a few guesses, but since there's no coordinated effort, and fringe ships have no clue what's going on might fear the worse, that Earth and the Federation have been assimilated, and flee, or be lured into the honey trap of going in to investigate, on at a time!
you could have a number of spawned adventures based on the theme.. trying to find allies, anyone who has a clue what's going on.. Maybe the Borg occasionally get the replicators on ships to begin replicating Borg Nanites, which attempt to assimilate people (Imagine if you drank Earl gray with Borg nanites in it!!!) You maybe would get pockets of resistance, such as many byanus, one of the few cultures able to fight off such a sophisticated virus, or an elite pocket cadre of scientists working to try and cure it, trapped at an institute. You'd have world wide problems, such as starvation, if all the replicator or even transport connections are not working (how do you get food about!) which would heavily waylay any ship flying by!
it would be a good way of giving the impression of 'the end of the world' without actually DOING it, (as I read in a game book recently, you can only blow up the world once!

) - there'd still be horrific challenges, a great deal of terror, the unknown and great danger, but a lot of it would be in the players heads, and from the general issues of complete communications breakdowns!
It's hard to imagine that the whole alpha and beta quadrant species we know wouldn't also be affected. The Klingons - definitely, they share the Federations communications technology. The Romulans probably, the Cardassians, depends on the era, but likely - we all grew up in each others pockets and share comms protocols, and stole each others' technology hehe
The Borg aren't just frightening because they are 'Zombies' but because of the technologies they wield!
