Originally i wasnt going to include borg in the mod, but Darkshimmer found a way to do it without making them look stupid. Like what all of the "professional" trek games did. Loki just happened to be working on a borg add on. So his inclusion was only natural.
The era for SoA 2 starts not long after the events of nemesis.
The Dominion played nothing more than lip service to the cease fire, and waited long enough to regroup its forces. Then came back to the alpha quadrant with a vengence. DS-9 is destroyed, cardassia has been enslaved again, and the breen happily re-joined their lost allies. The second dominion war is upon us.
The alliance between the Federation, Klingons, and Romulans is not as cozy as it once was during the 1st dominion war. Each individual empire can hold back the new dominion onslaught on thier own, Each thinks their own way is the right way. The only way. Mistrust, and petty differences shatter the alliance.
Meanwhile the borg transwarp hub was not completely destroyed as previously thought. Repairs were quick, and the hub is back online. The collective concluded that the alpha quadrant is too great of a threat for the quest to merely assimilate... Species 5618 must be annihilated. The borg must attack. Not with just one ship, but with the full force of the collective. While the alpha quadrant fights amongst themselves.
Not a bad prolog for someone who cant write a story if his life depended on it 