It has been six months sine the Federation and its allies drove back the Borg incursion into the Alpha Quadrant, wrestling the Omega Particle from the Borg Collective's grasp, and driving the Borg from Federation space Though the Quadrant is still recovering from the devastation brought about by the invasion, an emergency meeting of the Federation Council has directed Starfleet to find out how and where the Borg have been entering the Alpha Quadrant.
Once Found, the Federation forces have orders to launch the first ever offensive into the Delta Quadrant in their war with the Borg -a strategic operation to eliminate the Borg threat once and for all.
Such an operation carries risks- only some of which can be anticipated.
With the Federation's strength and attention focused on the Delta Quadrant, there are those in the Alpha Quadrant who might feel the time is right to reassert their power. While the forces of the Klingon Empire are be grudgingly left to play the role of Alpha Quadrant peacekeepers, they learn that it will take all of their strength- and their forces- to preserve the Quadrant.
In the Delta Quadrant, the Borg find themselves set upon by not just the intruders from the Alpha Quadrant, but by a merciless assault from the fluidic space dwellers, Species 8472"
From the Prelude in the Star Trek Armada 2 Manual
Star Trek Armada 2 is a sequel from the first Star Trek Armada. The Borg have returned with a new Assimilation weapon and have started another incursion of the Alpha Quadrant. Starfleet and Captain Jean-Luc Picard have now agreed to send a massive fleet in the Delta Quadrant to attack the Borg. The Cardassians use this opportunity to destroy what is left of Starfleet but the peace-keeping Klingons attempt to defend their allies by driving out the Cardassian. But an unknown rift has caused the ruthless Species 8472 to enter the Alpha Quadrant and are attempting destroy everything that is brought before them.