After Warp Squad 16 went missing, a detective (player) launched an investigation in an attempt to uncover what happened to them. The investigation is fully playable with audio-interviews and unlockable music here. The most germane information from the site has been collected below:
Warp Squad 16 (WS16) were an elite group of pilots who were responsible for protecting and expanding Alliance territory. Only the most skilled individuals are picked as possible Warp Squad candidates. Those picked are put through years of rigorous training, their personalities numbed by the process.
At the story's start we find out that WS16 are missing but no one seems to know why or how. However, the citizens of the worlds inside the Alliance are scared -- without WS16 to protect them, they are open to attacks.
To compound matters, we find out from the interviews and notes on the website, that the stars around the Alliance territory have started going out. From the pattern of extinguished stars it seems likely that the Alliance's own star will soon fall. With it, all life inside Alliance territory will end.
The cause of the stars dying seems related to an event where a member of Warp Squad 16 found an ancient artefact (that looked like a jackal) on an artificial dwarf-planet beyond the edge of Alliance territory. It is once the artefact is activated that the stars began to disappear .
The entire WS16 roster (with a new member enrolled to replace the one lost to the jackal artefact) were assembled and sent out to find the threat -- to work out what is killing the stars and to stop it. This is very unusual as it's rare 16 members are ever needed at the same time -- each are so powerful and skilled they can usually defeat threats alone.
The final interview sets the investigator up with a meeting with an Elder (hinted at being one of the original WS16 members from Earth from hundreds of years ago and somehow still alive).
Seemingly we are about to find out what happened to WS16.