Radicalized Malay Muslim co-pilot disables pilot, turns off transponders and communications, then heads west toward (?) (Pakistan, Mecca, Mumbai buildings?, Petronas Towers?). Aircraft rises and falls with fight in cockpit (like 9/11 Let’s Roll! heroes over Pennsylvania). Eventually crashes into Indian Ocean or a remote island.
The only system that wasn't turned of was not known about by the pilots because the service was part of the aircraft maintenance program which monitored the planes scheduled services to insure compliance. The airlines wished to rely on their service schedule however there is such a thing as CYA for Boeing.
Boeing was receiving data about aircraft maintenance and service to insure their scheduled maintenance was being performed by the airline.