PhilJet09 should be able to add some good info here.
The pilots have a flight plan filed, during the pre-flight activities one of the things done is to program the auto-pilot, setup the radio frequencies for the flight plan as well as the VOR frequencies for the land based parts of the flight. The aircraft is monitored by Primary Radar which is a simple blit on the Air Traffic Control radar screen, the farther off shore the higher the plane has to be to show on the radar screen. The plane is also monitored by a Secondary means using a transponder. When the plane is pinged it responds with flight information that can include some aircraft system information. Once out of Primary range the crew and plane still can communicate via many ways, including radios, ACARS reports, CPDLC, satellite phones, ADS-B, etc., some are automatic and some are manual.
All planes of this type have locked doors to the cockpit that can only be opened from the inside under normal situations. If anyone tries to break in the flight crew has time to issue an emergency code. The doors can be opened from the outside by entering an emergency code but again, the crew has time to issue an emergency code. The pilots would have time to set the transponder for code 7500 which is 'unlawful interference'.
All systems on the aircraft have protection and backup so spilling a cup of coffee into the flight controls can't shut down the airplane or a shorting radio can't take out the electrical system.
For the plane to be missing and quite possibly extremely off the flight plan a bunch of things need to happen. The auto-pilot has to be turned off and the plane manually piloted. These days there are GPS systems to back up the traditional navigation systems so there shouldn't be any confusion as to where the plane is and where it is headed. The communications and transponder has to be turned off or the system buss that powers it has to be turned off. The plane needs to descend below Primary radar of wait until out of Primary radar range. There has to be a deliberate non use of satellite phones, either voluntary or forced. If the plane is turning back across land it would show on Primary radar if someone was looking, but since it was flying off of any filed flight plan it could be missed. For the plane to be missing and on the flight plan there almost has to have been a quick emergency or virtually instant destruction. In the case of the French plane that went MIA a few years ago it was the flight crew that made several mistakes that led to the plane crashing in bad weather. There has been a recent push for more flight simulator training to prevent the errors that these pilots made.
There almost has to be someone that knows the 777 cockpit to achieve all the things that have occurred to hide the plane. To what end? Who knows, maybe it was a spectacular suicide along with a captive audience. Surprisingly there hasn't been any claim of terror, even if they had nothing to do with it. There was no extortion attempt. Time to look at flight insurance policies and see who took out the $10 million policy 30 minutes before the flight? It should be impossible for a commercial plane like a 777 to have a 'Payne Stewart' incident where lack of oxygen causes all aboard to loose conciseness yet that pattern does fit a lot of what we see with this flight. But, there is that troubling lack of transponder response.
