On the surface, this Klingon Duology is of immense importance to the franchise thanks to finally explaining why Klingons were smooth-headed in the original series but ridged in later incarnations (y'know, aside from the obvious).
"Affliction" kicks off the two-part story by tying into events depicted in the Augments Trilogy from earlier in the season, explaining rather handily that the Klingons were embarrassed by their brief encounter with genetically enhanced humans, and so pursued their own version of the program, creating Klingon Augments. Or trying really hard to.
They need Phlox to do it. That makes the Klingon Duology in name the Phlox story of the season. Except there's not a lot that makes it a Phlox story other than the fact that it technically features everyone's favorite Denobulan. That's mainly what brings both episodes in the story down a peg in my book, because it's disappointing, given that Phlox was a favorite character of mine and previously one of the best-used characters in the series.
There's other character work in the episode, though, and if roles had been reversed, could easily have boasted both efforts to full-recommendation status. The first is Tucker's transfer to the Columbia, under the command of Hernandez, previously featured in "Home." Aside from another great bit of continuity from the season, the development ties directly into Trip and T'Pol's constantly troubled relationship (that's the whole reason why he's no longer, at this point, engineer of the Enterprise, leaving the unimpressive Kelby to fill his boots).
And Reed receives perhaps some of his best material as a previous association with Section 31 (the covert ops group first seen in Deep Space Nine) proves to be an exceedingly uncomfortable conflict of interest.
In the past I've had a hard time digesting these episodes. There's just so much going on in them, a trend that works better in a later duology. But it's hard to deny their extreme importance. "Affliction" continues the fourth season ball rolling in very unusual but rewarding fashion. If only Phlox had had a more significant part!
franchise * series * essential * character
Memory Alpha summary.