In brief: A solid outing that covers a good amount of ground, although the cliffhanger concept seems a little unnecessary.
One nice aspect of "Affliction" is that the varied story ideas allow the episode to breathe. Often on this series, the focus is so narrowly put upon a few key characters and situations that it's either success for their specific arc, or bust. With "Affliction," there's a central plot line, yes, but there are also enough other things going on and enough people involved that we become interested in the characters and little details as well as the plot they inhabit.
And it never hurts to get back to Earth, which itself opens the series up to breathe a bit. The Enterprise has returned for the long-delayed launch of the Columbia, where Trip has been transferred to serve as chief engineer. Early in the episode, as he packs up to leave, T'Pol asks him if he's leaving the ship because of her. The answer is obviously yes, but he tersely tells her otherwise. What's a smitten man in this situation to do? I don't know, but it is kind interesting to see that the not-credible hooking up of these characters last season has now resulted in messy consequences. Let this be a lesson to future Star Trek generations: Don't sleep with your superior officer.
While on shore leave, Phlox and Hoshi are confronted on the street by ominous men in hoods. There's a brief scuffle (in which Hoshi's martial arts knowledge — as suddenly/retroactively revealed in "Observer Effect" — is exploited), and Phlox is shot and carried away. An investigation into Phlox's abduction is launched, beginning with interviews at the crime scene. With a little tweaking and additional insistence, perhaps this could've played as a teaser for CSI: San Francisco 2154. Or maybe Law & Order: Starfleet Security Unit.
As the investigation begins to sprawl, we're taken into some familiar Star Trek places. Hoshi's witnessing of the kidnapping doesn't turn up enough conclusive facts, so Archer suggests T'Pol perform a mind-meld to help Hoshi remember all the details. I guess this is like hypnosis, only better. When T'Pol expresses concern over her ability to initiate a mind-meld, Archer tells her, "I can walk you through it." I'm not sure what I think of that. It certainly makes sense on a plot level, arising from the events of "Kir'Shara," but do we really want the human teaching the Vulcan how to mind-meld?
The mind-meld produces a lead that has the Enterprise chasing a Rigellian ship to a space station that the Enterprise crew finds destroyed by the time they arrive. Destroyed by whom? Reed knows, but he's not saying.
On the other end of the plot, we already know that Phlox is in the hands of the Klingons, who are forcing him to help one of their doctors, a man named Antaak (John Schuck, not new to Klingon roles), research a cure to a deadly contagion threatening the Klingon population. Refreshingly, Antaak is not depicted as a villain but as a man of integrity — in spite of his adherence to accepted Klingon medical protocol, which permits the theft of data and resources and the "euthanasia" of live Klingon test subjects (a brutal notion played for mild laughs).
Through his search for a cure, Phlox learns that the outbreak began when the Klingons attempted to create genetically enhanced subjects from embryos discovered in the wreckage of the ship hijacked by the Augments (see "The Augments"). In terms of self-reference without literal self-reference, this will evidentially provide the explanation for the difference in appearance between the TOS Klingons and the Klingons from the feature films onward. The tie-in with the Augments arc is fairly clever.
Lt. Reed's investigation comprises the other major strand of the story, and the most intriguing. He discovers Starfleet's security grid was down at exactly the time of Phlox's kidnapping. When he tries to find out why, he's contacted by a mysterious agent (Eric Pierpoint, of Alien Nation fame). The show doesn't come out and say it, but this is clearly intended to be some version of Section 31 (their uniforms apparently won't change during the next 200 years; for the DS9 uninitiated, see "Inquisition"). Furthermore, Reed turns out to be a former Section agent. Because of the plot involving Phlox's kidnapping, Reed is reactivated by the Section, and ordered to thwart the Enterprise's investigation, for reasons we cannot yet be certain of.
Reed's conflict makes for the show's best drama, because it involves loyalty and betrayal. He's forced into hiding key evidence from Archer on the orders of an organization that he was apparently affiliated with before Starfleet. When he tells his Section contact that he's uncomfortable hiding things from Archer, the response comes back, "I suggest you adjust your comfort level." Eventually, a trail of clues leads T'Pol back through Reed's interference. Archer dresses him down and has him thrown into the brig as a traitor, which makes for some potent scenes.
Aboard the Columbia, Trip cracks the whip and tells the other engineers that the ship's engines will be online and ready for launch within the week. (He comes across as so inflexible that several engineers request transfers off the ship.) This is before he even reports to the captain for duty. The truth of these scenes are in the simple details of a man moving to a new post, and especially in the quiet observation of Captain Hernandez (Ada Maris), who seems to silently size Trip up while coming across as both professional and friendly. Maris' subtle and internalized performance is one of the show's highlights. Perhaps it's too early to say until we also see the action side of her character in command, but Hernandez already seems like a character that I could see as an anchor for its own series. Show me more.
In keeping with the show's effective "do a little bit of everything" approach, there's also a bizarre daydream involving Trip and T'Pol, which they both seem to share. The sharing goes even further: Hoshi has dreams of Trip, evidently because something spilled over from the mind-meld.
Then there's the action, where human-looking Klingons board the Enterprise and plant a computer virus, which has the effect of forcing the ship to accelerate out of control. Although one of the Klingons is captured, the MACOs still seem way too incompetent as security forces. As for the notion of the ship speeding out of control: Do we really need this as a cliffhanger, and isn't there something vaguely silly about it? (It begs someone to shout out: "We're going too FAST! We're gonna BLOW!")
My biggest fear is that the interesting stuff here will be all too casually reset in the follow-up. I'm speaking specifically of the fallout from Reed's betrayal and Trip having transferred to the Columbia. It seems to me that Reed can't remain in the brig forever, and we're not about to see Trip on an ongoing, parallel Star Trek: Columbia. Hopefully, however they resolve these matters will be worthwhile.
Like many outings this season on Enterprise, "Affliction" is solid and entertaining, but with no real signs of greatness. This, unfortunately, limits my review to another where I basically say "here's what happened in the episode" and "I mostly liked what I saw." Deep analysis or heavy thought doesn't really seem to be required. Not that that's a problem.
Next week: The Enterprise keeps accelerating until it explodes. Okay, probably not.
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