"E.B.E." is one of the 5 mytharc episodes of the first season and like the rest of them, we learn almost nothing new. There are certain conditions to rely on in each episode. The government is involved, there are bright lights, people lie to Mulder and Scully, and they have no idea what they are dealing with, though, presumably it is aliens.
After investigating a UFO sighting in Tennessee, Mulder and Scully track a truck across the country which may be carrying an "extraterrestrial biological entity," e.b.e. for short. They end up at a power plant in Washington where Deep Throat is waiting. He tells Mulder that after Roswell, several countries, including the United States, agreed to kill any alien life form. Deep Throat killed an alien during the Vietnam War which is why he goes to Mulder for atonement. At face value it's interesting and has potential for more--and I'm not sure how to review an episode like this--but knowing what happens later on kind of puts a damper on any excitement I would have over the developments.
While the alien stuff in the episode isn't important, what the government does it more significant. Mulder and Scully find the government tapping their phones and listening closely to their conversations. Even Deep Throat admits to deceiving them, admitting that a lie is best placed between two truths, which doesn't really make sense.
The Lone Gunmen make their first appearance in the series and through in a couple fun, kooky lines. The good thing is, they'll be back many other times.
"E.B.E." is another example of Chris Carter stumbling through the darkness. He has ideas about aliens and government, and has dialogue to play up that angle, but he can't apply it in a cohesive manner.
Score: 8.6/10