From the evidence I've seen so far, my best guess is that the two guys with the stolen passports were aliens and they called in pickup from the mother ship. The guy operating the transporter beam couldn't tell his fellow aliens apart from the humans due to the aliens being in human form down to the genetic level, and just transported the entire plane instead. The human passengers were quickly gassed and are stored in hibernation for future experiment fodder. Expect alien abductions to drop dramatically for the next several years as they now have a full compliment of test subjects.
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