"Deep Throat" is like a continuation of the pilot. It cements the notion about aliens and a government cover up through another hazy story which ends up unresolved while Mulder and Scully continue to feel each other out. Scully is still the skeptic and Mulder is still the believer, and we see just how fervent of a believer Mulder is.
And in that sense, there really isn't much to say about the episode. The major development is the introduction of Deep Throat, a character who is important in the first season and basically confirms to Mulder that there are aliens. One of the big problems with the mythology is that we don't really know why Deep Throat didn't want Mulder to take the case in the first place. The stuff that goes on behind the scenes never comes together and we are left to ponder exactly what people are thinking. In this instance, my thought is that Deep Throat knew the case would end nowhere and only wants Mulder to pick battles he can win.
The plot is fairly simple and effective. Air force pilots flying experimental aircraft come back messed up, leading Mulder and Scully to Ellens Air Force Base. The first of many times Mulder runs off without Scully ends with Mulder captured. However, Scully is no pushover and is willing to pull her gun out and make some demands to get him back. I love how this is firmly established in the second episode. Scully is willing to risk her life and threaten others to keep Mulder safe. Right now, she's doing it mostly out of a sense of duty for her partner, but we see the personal bond grow over time.
One of my favorite part of the episode is Seth Green and his stoner friend, both of whom are gladly accepted by Mulder as legitimate sources of information. The humor of The X-Files can be sweet and not over the top as show in this case.
I was planning on doing 3 episodes today, but I'm kind of tired and this is a natural stopping point before the monster of the week episodes, so only 2 episodes today.
Score: 9.2/10