Nexus: The Jupiter Incident
Approximately 5000 years before modern man, there were the 'Creators', who were a highly advanced alien race. They created an artificial intelligence that possessed an evolution algorithm. This AI eventually broke free and developed into an artificial god. The god then proceeded to transform the galaxy according to its own need, even taking control of its own creators.
3000 years later, a small group of still free Creators reached the Sol System in the vessel that later became known as the Angelwing. They then started their grand plan to stop the artificial god. Over the next 2000 years they worked on the plan, while also guiding humanity from a distance.
In the Earth year 1962, the last of the Creators race perished, but their plan was still going on. They realized that the only way to defeat the artificial god was to create something much like it. So in their base near Pluto, they left behind a seed that would one day create that which would be the only hope of winning.
2112, the Angelwing was captured from the Kisaki Syndicate by Marcus Cromwell. It was then sent to explore the Syndicate base near Pluto. They discovered the Creator's base, a wormhole and a dormant Mechanoid. During the investigation of the area, the Mechanoid reactivateed and began to attack the Angelwing. The ship was saved when Angel transfered herself from the base to the ship and activated the shields. She then proceeded to instruct the crew to take the ship into the wormhole. On the other side they found the decendants of the Noah expedition, along with two alien races. They joined the Noah Defense Forces in the fight against the Gorg.
4 months later, the Angelwing headed to an asteroid field to study a completely inactive Mechanoid body. Angel then proceeded to use the ship's assimilation abilities to merge the Mechanoid with the Angelwing. This gave the Angelwing some new abilities, and also created a brief connection between Angel and the Entity. This connection was enough for Angel to be corrupted, though she hid it from the crew.
2113, the final battle against the Mechanoids and the Entity began. It was at this time that Angel revealed her new self to the crew, just before forcing them off the ship. Only Commander Sweetwater remained, she had gradually been corrupted by Angel through the implants given to her by the Ghosts. Angel transfered the new crew she had put together, those that thought like her, and proceeded into the Nexus.
This theme is not entirely canon but for all intents and purposes it follows the game exactly up until the last battle. So it's pretty close. More information about the source (along with links to official sites) can be found at: