The Omega's artificial intelligence, or OMAI for short, is programmed to be polite, reassuring, efficient and relentlessly upbeat. It is also programmed to protect the Omega's mission above all else, which is splendid when all is going to plan, less so if it perceives the Omega's own human crew as a threat to the mission's success. In the initial Challenge Deck supplied with SSO this is exactly what has occurred, the OMAI has murdered the entire original crew and is quite determined to do the same to you. It will attempt to do this in two general ways, using its ability to Vent Oxygen, since it has control over the supply and doesn't need to breath, this is a fairly efficient method for it to wipe out all your crew in one go. However there is a lot of oxygen, at first, and it can't stop crew from using systems to produce more so the OMAI will also tend to Shutdown locations, killing all crew within.
Crew can reboot locations by hacking the A.I. in the Computer Module and avoid being targeted all at once by spreading throughout the ship but these are ultimately temporary measures. They can attempt to simply stop accessing OMAI's systems but once you know your ship is being run by any form of murderous A.I. there's really only one way out, pulling the chips and shutting down the main frame. By Shutting Down Higher A.I. Functions players can skip fully one sixth of the Challenge Deck, or a third if they have the Radio Officer in place. But to do so comes with a terrible cost, since the only way to be sure of shutting off the Computer Module is to be in there when it happens.
The mission above all, and remember, Your Sacrifice Will be Appreciated.