Another RTS game like the original, it showcases the events in the Alpha Quadrant between the United Federation of Planets, the Klingon Empire, the Romulan Star Empire, the Cardassian Union, Species 8472, and the Borg.
A few months after the events of Star Trek: Armada, the Borg are at it again. This time, they've created fast assimilation pyramids that assimilate entire worlds instantly.
The Enterprise-E and Starfleet Command has had just about enough of the Borg and, after they seize control of a transwarp conduit, attempt to launch a counter-offensive into the Delta Quadrant, Borg space.
While the Federation mounts its attack, the Klingon Empire finds out that the Cardassian Union is planning a strike of its own in the Alpha Quadrant, so the Klingons and Cardassians go head-to-head.
Meanwhile the Borg discover that Species 8472 has found a way to the Alpha Quadrant. The Borg Queen realizes that they need the Federation's help to defeat Species 8472.