Starfleet Command III: Story Synopsis

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Starfleet Command 3 takes place after Voyager's return to the Alpha Quadrant.  The Klingon Empire and United Federation of planets have begun the construction of Unity 1, a starbase capable to detecting cloaked vessels, even in the neutral zone.  This would cause a shift in power away from the Romulans, and ultimately leads to conflict... 

In the Klingon Campaign, the Rakelli, a civilization defeated by the Klingons decades ago, reappear and begin attacking Klingon interests.  However, this proves to be the least of the Empire's problems when your own brother Jureth leads a rogue group to attack and cripple the Unity station...

Unfortunately for the Romulans, the Klingon attack on the Unity station failed.  Arai, leader of the Tal'Shiar, recruits you to train as an agent.  Using recently acquired Federation technology that allows your ships to masquerade as Klingon or Federation ships, you set out to attack both the Alliance's installations.  This causes a rift in the Federation-Klingon alliance that allows you to lead the mission that destroys the Unity station.

With Unity destroyed and the Federation-Klingon alliance falling apart, Captain Picard leads an investigation into the attacks.  You ultimately determine the Romulans involvement and lead several task forces that strike at the heart of Romulan Empire and deal a crippling blow to the Tal'Shiar.  Upon the Arai's death, the Praetor of the Romulan Empire reveals that the Tal'Shiar was not acting on behalf of the Empire...

The above campaigns represent only part of the game.  Between missions you can choose to take on other missions in which various situations will arise including responding to distress calls, scanning star systems, and protecting ships.  In the Nemesis add-on pack you actually get to test out the Scimitar before Praetor Shinzon takes command...