The Borg Queen, stranded in the Alpha Quadrant by the same twist of fate that trapped Picard on her side of the galaxy, discovers that Species 8472 has found a way into the Alpha Quadrant. In the final battle, Martok tracks down and kills Gul Kentar, taking out the Quantum Singularity Project along the way.

The Klingons stop the Cardassian rebellion and occupy their homeworld, Cardassia Prime.

Martok leads an attempt to thwart Kentar's grab for power and destroy the project. Kentar is developing a 'Quantum Singularity Ship' that allows the Cardassians to summon Species 8472 ships at will. Klingon Chancellor Martok discovers that Gul Kentar, leader of the Cardassian uprising, is in league with the Romulans. The Cardassians proceed to destroy the Federation's reserve fleet. Meanwhile, the Cardassians use the sudden absence of Federation forces to begin their own offensive. Though successful, some of the Federation forces, Picard included, are left stranded when the Transwarp Portal collapses due to a destabilization of the inter-spatial transwarp manifolds. Starfleet Command then orders Picard to seize control of it and launch a counteroffensive into the heart of Borg space in the Delta Quadrant, into the Borg staging grounds.

Intrigued, Picard discovers a new type of transwarp gate called a Transwarp Portal, capable of sending fleets of starships from one quadrant to another almost instantly, explaining how the Borg managed to get so deep into the Alpha Quadrant undetected. After routing the attempted foothold, Captain Picard discovers a new type of nebula: a tachyon nebula. They have created a new ship capable of assimilating entire worlds in just a few seconds. Set just six months after the events of Star Trek: Armada, the Borg once again threaten the Alpha Quadrant. The game showcases 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.

Like its predecessor, Armada II is set in the Star Trek: The Next Generation era of the Star Trek universe. It was the first of the three major Star Trek video game sequel titles that were released by Activision from 2001 until their departure from the franchise in 2003. Star Trek: Armada II was released by Activision a year after they acquired the full rights to all the franchise holding of the video game's franchise from Viacom. The game was developed by Mad Doc Software. Star Trek: Armada II is a real-time strategy video game published by Activision in 2001, based upon the Star Trek universe.

Star trek armada ii win 7 x64