What are the chances of a cover up where by intelligence services of some country found out some terrorists were going to be on board. To not alert other people in their organisation they were captured they fake a plane going missing. Have agents on board, take these guys during the flight, turn off transponder, fly under radar(is that remotely plausible, or would turning off transponder/comms allow them to fly to a secure airport without being tracked with the right routes and the right radar taken offline or something) or otherwise avoid tracking. Land somewhere, they keep everyone secure and on site. This would allow them to question some lets presume seriously important suspects without certain high up targets being aware they were possibly compromised, giving them time to get info and potentially capture targets before they decide to change locations because they think these guys are in custody?
The opposite take on the same story would be a hijacking, a great plan to land the plane without being tracked and get 200 hostages in an insanely difficult to rescue situation before claiming responsibility and making demands.