The plot jumped all over the place, trying to encompass as much as it could. There were Mavericks, old CorSec agents running about, new enemies trying to stake a claim, the Tsivrixsh Empire, and finally foes that came from the weirdest of places.
From Point A to B, the focus was of the team having to leave Earth and set out into the galaxy to find allies to stop the Tsivrixsh. When they finally accomplished this, the organization called itself The Alliance and brought the war to the Tsivrixsh Homeworld, where the climatic battle took place.
By the end of the RPG, the Tsivrixsh was under a new government and the Alliance was attempting to become more stable and help protect the galaxy from other races hoping to expand.
In actuality, though that was the end of the main story, the next ten years of the main characters'lives were focused on and how they dealt with the changing era, finally ending up with a huge battle by their greatest enemy: Xevil.