Ok here's my theory (get your tin hats, and religious hatred ready fellas...)
Most christians believe that before Jesus returns to judge the earth (the second coming) there will something called 'The Rapture' (a name not biblical but alluded to).
Basically true believers will be extracted from the earth in the blink of an eye, to meet with Jesus in the air.
The AntiChrist will need a way to explain millions of people just dissapearing, so will probably use theories such as mass alien abduction to get peoples attention away from the bible propechy - crazy right!!!
Not if you've prepared the ground correctly, you know, the odd plane here and there for a few years, maybe a coach load of people that can't be found/explained......
The poor passengers are probably dead somewhere in a disused airfield in Vietnam, while the aircraft is being carefully disposed of.
'Alien abduction' number 1 folks.