Even he wasn’t consciously aping it, Frank Spotnitz was evidently inspired by just how well the previous season’s close-quarters encounter between Mulder and Duane Barry worked, and decided he’d have some of that. Hence Mulder trapped in a train car, ticking down to its detonation, with a man who just tried to kill him. It helps that Stephen McHattie, despite being cast as a standard heavy/assassin, is a terrific actor, as it ensures the stakes here feel very genuine.
X: There are limits to my knowledge.
Scully: I don't have time for your convenient ignorance.
Scully’s very much on the reactive front, being fed what she wants to hear – that there are no aliens – by Don S Williams’ First Elder. And forwarding that on to Mulder is inevitably going to create some tension between them. In theory, her credulity of the enemy, telling her the disfigured individuals who have been shot dead, toppling into mass graves – quite strong stuff, even for the show’s permissive tastes – were subjected to various terrible diseases and radiation tests, and that the fellow aboard Mulder’s train has haemorrhagic fever (oh, that). That this is mixed and muddled with a leper colony – Hansen’s Disease – adds to the overriding confusion (Colin Cunningham’s victim Escalante, brought on as an exposition vehicle, is perhaps the episode sounding a rare clumsy note).
Mulder: You know what I think? I think you're a liar. I don't think you work for the NSA, and I don't think there's a bomb on this train.
Quite apart from these lies, we have Mulder’s conjecture regarding the purpose of the experiments. There’s no particular reason to believe the Red-Haired Man is telling the truth, particular since there’s so much scientific fraud with regard to his picks (star wars, the atomic bomb, the most advanced biological weapons). Quite what kind of immunity a hybrid is supposed to have to star-wars tech, I don’t know, and one wonders how such goals fit in with hybrid immunity to disease/radiation generally. Even if he’s telling the gospel truth, the prevailing quagmire of disinformation is precisely what will eventually lead to Season Five Mulder becoming convinced it’s all a big sham. In my view, this is also where the series is at its most germane to the real world’s “ET” game, when it’s admitting that everything you hear is a deception (which in turn leads to the conspicuous hole in the show’s exploration of its theme: John Keel’s ultraterrestrials).
Scully: What I am saying, Mulder, is that there is no such thing as alien abduction.
Nevertheless, Scully’s thick-headedness in 731 does otherwise take the biscuit, particularly since she needs coaxing by X to go investigate what anyone with the FBI’s resources/contacts should have done the first instant they retrieved the chip: get it investigated. That it offers some particularly transhumanist capacities (if it can collect information – “know a person’s every thought” – one might logically infer it may also be able to interfere with, augment or direct thought. These scenes also see the first appearance of Agent Pendrell (Brendan Beiser) and his klutziness around Scully: “Keep it up yourself”).
Mulder: I know what I saw on that train car. It wasn't a leper and it wasn't human.
The best of the episode, however, concerns Mulder first doing his own Narrow Margin on the train, pressing Muchael Puttonen’s Conductor into service, and then having some one-on-one time with the Red-Haired Man. Rob Bowman really knocks 731 one out of the park with the rising tension and paranoia, as Mulder has to sift through his captive’s lies and half-truths. In contrast to Duane Barry’s sympathetic understanding, there’s no meeting of minds here, but the material crackles for different reasons. And it’s a neat touch that the Red-Haired Man is simply biding his time, pretending to be supplicant until he can get out of his prison.
Mulder: Scully, let me tell you, you haven't seen America till you've seen it from a train.
X’s crowning moment comes here too, of course. He intervenes decisively, blowing the not-NSA man (Malcolm Gerlach according to the DVD collection) away and carrying Mulder to safety before the train car explodes; Mulder was under the assumption that, this being an alien-human hybrid, the Syndicate would want it back (whereas Scully’s assumption was that, it being a plague carrier, they would not); the Red-Haired Man says as much. So in closing at least, it would seem the argument shakes out on Scully’s side, that Mulder is indeed chasing aliens that aren’t there (like every UFOlogist). Of course, the explanation could simply be that this particular alien-human hybrid is not that special, that it is not alone, and thus that it did not need saving.
Mulder: I, I don't need an apology for the lies. I, I don't care about the fictions they create to cover their crimes. I want them accountable for what did happen. I want an apology for the truth.
It’s indicative of where the show’s strengths really lay that, despite all the action theatrics and gruesome prosthetics, the real meat of 731 consists of two people having a battle of wits. A conversation. And not one of didactic exposition (one of the show’s fatal weaknesses). As much as we know Mulder has to be right, as much as we know the makers need to keep the aliens bubbling under, the show wisely preserves the shadowy realm that results from being shut out of the inner sanctum (when it does invite us into the machinations of the Syndicate, it is invariably underwhelming). 731 is the conspiracy arc at its very best.