Master Override is the top level of Security Clearance on the Ishimura, but unlike the other levels, you won't just get it by progressing through the story. You'll have to complete the You Are Not Authorised side quest that unlocks in the Captain's Nest on the Bridge Deck when you see Hammond there during chapter four.
The quest requires you to locate Crew Rigs in the different sections of the Ishimura and then return to the Captain's Nest to create your Master Override clearance. It's worth noting that Master Override containers hold Dead Space weapon upgrades, so that's the primary reason to unlock it.