Buried within the core operating system of the Omega is an absolute over-ride, all the living crew are expendable should the computer decide they are detrimental to the mission.
The AI Challenge Deck is provided with the SSO base set and tells the story of the OMAI's attempt to kill off your rescue crew, primarily by venting your oxygen supply (computers don't need to breathe) and shutting parts of the ship down.
The crew have multiple options to respond, they can reboot locations by hacking the Computer Module, spread out to protect against location shut down and desperately work to produce more oxygen, but these are all temporary measures.
Once you know your ship is being run by any form of murderous AI there's really only one way out, pulling the chips and shutting down the main frame. But to do so comes with a terrible cost, the only way to be sure of shutting down the Computer Module is to be in there when it happens.
Survival or sacrifice, hero or victim, rest assured that the Omega sees all, the Omega never forgets and Your Sacrifice Is Appreciated.
Whether HAL from 2001: A Space Odyssey or MUTHR from Alien, if your deep space vessel has an AI central operating system then things can go wrong, and the Omega's AI, or OMAI, is no exception.