Space Pirates and Zombies

Humanity has expanded throughout the galaxy after the discovery of the miraculous Element 126, colloquially known as 'Rez', which enabled matter replication technology (including cloning), advanced artificial intelligence and faster than light travel in the form of the warp gate network. With more of the new element found near the galactic core, the outer worlds, including Earth, have become neglected backwaters. With humanity now numbering in the thousands of trillions across thousands of planets, the spread of interplanetary diseases caused the collapse of many human governments. A totalitarian militaristic police force called the United Terran Alliance (or UTA) stepped in to fill the void and began to strictly police access to the warp gates. Civilian access to interstellar travel was abolished in what was described as a 'temporary move' but this state of affairs has existed for over 1000 years. With humanity living in the decaying remnants of its past glory the civilian populations of many sectors rose up against the UTA in the vicious 'Lockdown Wars' over control of space travel and the supply of Rez.
According to the game's lore, a hidden motherlode of Rez is believed to exist in the galactic core, although no one has found it. Miners and pirates in the Earth system unite to challenge the UTA in an attempt to locate it.

Plot

For years the Pirates of the Earth system, under the command of explorer Don Gibson, second-in-command Elsa Young and former UTA scientist Dr. Carl Memford, have been constructing a massive armed mothership named the Clockwork to take on the warring UTA and Civilian fleets between them and the galactic core. After allying with the Rez miners in the Earth system, the Clockwork crew blast their way through the UTA blockade at the system's warp gate and head into the wider galaxy. This brings them into conflict with the high ranking UTA commander Admiral Jamison who doggedly attempts to stop them reaching the heavily guarded Core Worlds.
After acquiring the technology necessary to access the Core Worlds the Clockwork crew discover that the Core Worlds are overrun with a horrific biomechanical pandemic that fuses living tissue into ship systems to create an all consuming hiveminded fleet of Zombies. It becomes apparent that the UTA had been battling this infection for over 200 years and the added security measures for accessing the Core Worlds were not to keep Civilians and Pirates out but to keep the Zombie infection in. The Clockwork battles on and eventually discovers a hidden alien warp gate into the galactic center - there it discovers an extremely ancient and hostile alien intelligence known as the 'Dark Entity' which is both the source of all Rez in the galaxy and the controlling intelligence of the Zombies.
To the horror of his crew, Captain Don Gibson immediately defects to the Dark Entity and the Clockwork is infected and transformed into a Zombie superweapon. The remaining crew are only saved by the intervention of Admiral Jamison, who then retreats in shock. Don reveals that he had encountered the Dark Entity over 200 years ago and was enslaved and dispatched as a means of securing the success of its infection by destroying the UTA's blockade on interstellar travel, with the Entity prolonging his lifespan in order to do so.
The Zombie infection quickly spreads throughout the entire galaxy, with the crew of the Clockwork becoming widely hated and cursed for bringing about the apparent end of humanity. Seeking to save the galaxy, and to get revenge on Gibson, Elsa Young takes command of the Pirates and spends the next 2 years creating a new mothership - Clockwork 2. With the help of Admiral Jamison and other allies, the Pirate fleet fights its way back through Zombie space to the realm of the Dark Entity and destroys it, Gibson and the original Clockwork.
The fate of humanity is left in question, as the Rez it so desperately depended on can now no longer be replenished. Choosing not to dwell on this the Pirates instead devote themselves to destroying every trace of the Zombie infection.