A dramatic increase in UFO sightings and a bizarre attack on a transport truck convince Mulder that he's on the trail of a live alien being covertly transported cross-country. For her part, Scully, equally wary of the involvement of the Lone Gunmen as she is of Deep Throat, suspects a rather more earthly explanation.
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For anyone who didn't get it, an E.B.E. is an extraterrestrial biological entity aka a live alien.