There are two primary characters in Little Green Men: John Oliver Banion and Nathan Scrubbs. Both of them are involved with governmental programs regarding extra-terrestrial visits to earth, but both of them are quite different.
John Oliver Banion, often referred to as simply "Banion," feels himself to be very powerful politically both through his weekly talk show and through his intellectual prowess. He prides himself on tearing into his guests and cutting them down to size. On the golf course one day (and as a result of Scrubbs previous devastation) Banion sees a space ship as well as aliens who he is unable to communicate with. Because he loses consciousness at various times during the encounter and because of the advice of his wife, Banion eventually denies the claims that he has been "abducted." Banion is abducted yet again on the way to give a speech. When released, his abduction becomes the focus of this speech as well as his life. This causes him to lose his TV show and start another focusing on aliens. After being contacted by Scrubbs, Banion finally learns the truth; however, he is eventually blamed for the explosion of the new space station. Charges against him are finally dropped when a fake photo appears of "aliens" destroying the station.
On the other hand, Scrubbs has worked for the governmental abductions unit for the Majestic Twelve (a classified program) for a couple of years. Scrubbs is sick of working in the Majestic Twelve (as he originally wanted a spot in the CIA) and asks for a transfer from the alien abductions unit. After being rejected, Scrubbs is devastated. At this point, Scrubbs sees Banion tearing apart one of of his guests on TV and decides that Banion deserves to be "abducted." After Banion's first abduction is unsuccessful, Scrubbs plans another. This second abduction makes UFOs the focus of television and gets Scrubbs in trouble. Scrubbs finally contacts Banion in order to stop the madness that ensues.