The recent events of Star Trek: Alien Domain have come to an end. Several fleets have returned from fluidic space, and warned Starfleet and its allies about the continued threat of Species 8472. The Klingon forces have returned to their territory to plan, and regroup. Following those events, nothing related to the 8472 incident has happened since. However, tensions are rising underneath the surface.

Reports surface from Federation scouts in the Gamma Quadrant that strange wormholes were appearing, and Federation allied forces in the area have been going missing. Starfleet command believes it to be Species 8472 making its move, and trying once again to enter our space. Starfleet sends a captain (player) who survived the trials of fluidic space to oversee the construction of a new starbase being built on the other side of the Bajoran wormhole, in the Gamma Quadrant.

A new rogue faction comprised of former Dominion members have sent forces to the strange wormhole, only to have them disappear as well. Blaming the Federation for bringing this trouble to their home, this faction uses it as an excuse to begin a new conflict with the Federation forces.

Both sides must not only face each other, but also must prepare to face 8472’s forces from fluidic space.