The key points were that the IFF on TWA800 was disabled. There was apparently a target drone fired behind TWA800 and the shooter was in direct line with the target drone and TWA800 when the shot was fired. (according to the radar tracks)
A couple clinton enemies were on the flight so it could have been staged to arkancide them and yet look like an accident. All it took was a confusion about which miliary exercise areas were active, a target drone fired to be in the right place at the wrong time and a little sabotage of the iff transmitter on the flight.
Read the research thread for the discussion. (warning, it is a long and detailed read).
I can't fathom that even the x42s would ever consider offing a planeload of Americans to get a few of their enemies. Also, to have the drone in line and all the other technical stuff happen in a planned manner stretches believability.
I guess an awful accident caused by a few individuals screwing up their jobs makes the most sense to me.