What's cunning about the "Nisei/731" story is not so much the 'answers' revealed but the way that it brings us back around almost to where we began two years ago--Mulder believes in the alien abduction story, Scully does not. It's more like a spiral, which does not quite return to its point of origin, than a circle: while Scully is still a skeptic she is a skeptic in a more plausible way. She no longer rejects the 'evidence' before her out of hand, but tries to fit it into her own theory of medical experimentation and research atrocities. I am glad to see that we must not return to Scully as Spock ("Mulder, that is so illogical."); she retains not only integrity as a character but her own unique voice. To make her a believer seeking only the evidence to bring an alien into court would make her an echo of Mulder, and she deserves better. Season One told the stories pretty much through Scully's eyes. Season Two told them through Mulder's eyes. Now we are reaching a point of equilibrium where both characters carry plausibility.
The scariest thing in "Nisei/731", however, is not the pitiful lepers or the alien bodies piled in a pit, in a scene reminiscent of "Schindler's List". No, the scariest monster in this story is Dr. Ishimaru, the Japanese version of Dr. Mengele, the counterpart to the Dr. Klemper we saw in "Paper Clip". The ultimate abstraction of the scientific principle, with no soul, no heart, and no mercy, he embodies the fears of a society that has yet to come to grips with the technological wonders in its hands. In any case, we are treated in "Nisei/731" to a peek over the edge of that abyss opening before our feet with the advent of genetic engineering. Our fears are not so much of the technology but of the men who wield it: Dr. Ishimaru, Dr. Klemper.
Stephen McHattie acquitted himself more than admirably as the relentless, arrogant assassin sent to kill Ishimaru and the quarantined passenger. It's a shame he dies as I believe he could have been a great recurring character. His lean, skull-like face lends itself automatically to menace, and he can deliver a truth in such a way as to convince you it is a lie. The little conductor was absolutely wonderful in his rabbity way, and having Gillian Barber playing Penny Northern so she could say "She is one" was hilarious (Barber played Beth Kane in "Red Museum"; "He is one" was a catch phrase for that episode. I wonder if I'm the only one who caught that reference).
David Nutter, who directed "Nisei", uses closeups better than anyone else on this series. His painterly and intimate portraits bring the viewer right into the character's emotions.
Rob Bowman, who directed "731", set up some wonderful shots: the low angle on the leper dormitory hideout room, the death squad truck bursting the gate, the heartbreaking open grave in the leper colony. Both directors used reflections in interesting ways: I liked the scene in "Nisei" when the Japanese diplomat's face is reflected in the interrogation room window against Walter Skinner, the television reflecting the whole living room in "731". Bowman even combined both techniques by having the alien passenger in the boxcar reflected in an extreme close-up of Mulder's eye, a shot that took us right into Mulder's head.
I have to mention Mark Snow's mournful and poignant score, particularly in the scene where Scully discovers the bodies of the leper colony victims. Once again so much of the mood and atmosphere that help suspend our disbelief depends on a score that keeps us on the edge of emotion.
In the final analysis, this is a well put together execution of a top-notch story. The ground for "Nisei/731" was pretty well laid in "Anasazi/Blessing Way/Paper Clip". The only minor flaw in this story arc for me was that Mulder and Scully were separated too much by the plot.