My guess, a small fire in the E&E bay caused the electronic equipment to fail in such a way as to depressurize the aircraft slowly (or just not pressurize the aircraft) while not sending a signal to the cockpit (I think there was a Lear jet or two this happened to) and also cutting communication (both voice and data). The low pressure causes the E&E fire to extinguish before effecting more systems (like the autopilot), everyone on the plane passes out, it continues to fly until it runs out of fuel, ditching in the ocean. The ditching keeps the debris field small (as opposed to crashing on land and taking out a mile of trees with fires burning for a couple of days), anything that might have floated becomes waterlogged and sinks in the days following while the SAR folks are looking in the wrong location. Not much of an oil / fuel slick to begin with because the aircraft burned all the fuel, and the seas are rough enough in that area to remove / dissipate any small floating oil product pretty quickly. The Indian Ocean is very deep off the North West coast of Australia, so anything that sank would be difficult to locate, and may never wash up. Even if something does wash up on one of those little islands (Christmas or Cocos), even if someone does find it, they may think its just more jetsum garbage. In other words, it's gone and I doubt we will ever find the black boxes, or know for sure what happened. Modern mystery that is not going to be solved.
EDIT: Alternatively, the pilots smelled the electrical fire and shut all electrical equipment off then started turning each system on one by one looking for the cause and became distracted, failed to notice the plane depressurize, passed out, and the rest per above.