You know what?
I think Pandorium Survivor needs a prequel, the part where the battlecruiser have not entered the station.
Starting Story 0-3:
We could be the rag-tag group of recently recruited crew of the battlecruiser who is attracted by the high payout (due to circumstances the battlecruiser has lost much crew but it is kept secret by order of the battlecruiser's admiral or captain) who is transporting unknown top-secret "cargo" (the monstrsity from somewhere leave it to your imagination) and experimental equipment (example is some of those special weapons found around the station) however something alien has impregnated one of its crew (the origins of this alien could have been from the same place where the monstrity was obtain as a cargo from, example research station).
Story 1-1 (x-1 Story branch):
The battlecruiser (shorten to BC from now on) drop out from hyperspace and docked with the station Pandorium which is orbiting a nearby planet (name of planet leave to your imagination), the crew is carrying out their duties of resupplying and refueling the BC. (Experimental equipment is already on BC)
Story 1-2 (x-2 Story branch, alternative):
The battlecruiser (shorten to BC from now on) after securing its unknown top-secret cargo from the research facility and replacing its crew that was lost from ??? (what you call those ports for spaceships on planet's surface?), left the planet's surface and docked with the station Pandorium which is orbiting a nearby planet (name of planet leave to your imagination), the crew is carrying out their duties of resupplying and refueling the BC. (Experimental equipment is from Pandorium in process of transporting them to BC)
Story 2-3 (Story 1-1 and Story 1-2 branches path here as x-3):
Due to issues on the BC power generator (the alien hatched... you know what happens next) the admiral or captain of the BC made a decision to move the "cargo" to station Pandorium because it requires power to contain the content inside it along with its experimental equipment that could help restraint "it" if it ever broke out of containment.
As the alien issue on the BC that the admiral/captain tried to keep secret from the new crew members became worse and worse, they started to notice that something is amiss, soon the BC emergency alarm goes off as critical systems around the BC are being destroyed by the aliens on board (prelude for the Pandorium Survivor game where we need to find BC parts and Hydrolic Frame to fix the BC), all hell broke loose on board the BC.
To be continue...? (I stop here for now, tell me what you think xD)