Simply turning a transponder off is not going to make a modern airliner disappear; there are too many systems sending information into the ether. On Airbus the loss of all electrics is regarded as impossible but some major power failures have happened. I'm not sure how the 777 is configured electrically, but a major electrical failure or fire in the E&E bay might cut all the aircraft communication systems and leave the crew poorly placed in the middle of the night.