"Apology is policy."
REVIEW: It's getting harder and harder to figure out who's on a who's side, but if we take everything at face value, here's what we think we know. The Syndicate is behind so-called "alien abductions", and trying to find a way to create super-soldier human/alien hybrids. Many of the experiments are geared to making these soldiers immune to radiation and diseases, which is no doubt why some abductees are dying from unknown cancers. The experiments are conducted by former 731 scientists, a historical Japanese group that committed atrocities in World War II. Roped into serving the U.S. government as part of Operation Paper Clip, their loyalty is still to Japan, and they've gone rogue, taking their one perfect specimen back to their home country. The Syndicate retaliates by sending death squads to kill all the scientists and subjects, and retrieving the work. Shiro Zama, the head guy, is finally killed by an assassin that kind of looks like Robert Patrick, who claims to be NSA, but is working with for the Syndicate. However, the Syndicate is unable to retrieve the super-soldier, though they do get their hands on Zama's notes to Mulder's dismay. I think that's it. When people go rogue inside the Conspiracy, it's hard to tell if there's actually another faction at work, or if it's just rebellion. X is the same. Is he working from a second organization (Deep Throat's authority seemed to imply this), or is he employed by the Syndicate and working against its interests from within (probable).
One thing's for sure, the mytharc is steeped in Axis imagery. In Anasazi, we saw a boxcar full of failed hybrids' bodies, and here, the attendant death camp, with its open graves. The hybrids' large craniums evoke the emaciated, shaved bodies of concentration camp victims. It's not just that the Syndicate is employing former "butchers", but that history seems to be visually repeating as well. So it follows that the action would take place on the slightly retro world of a single train, an interesting environment with a strong geography. (Kept thinking Mulder would get the conductor killed, though.) Mulder acts heroically, if foolishly, and his fatalism when he believes all is lost is a bit touching. It's easy to manufacture suspense with a ticking bomb, but the way Mulder and the Red-Haired Man interact is full of choreographed tension; they're working harder than the clock on this one.
But there are some accidentally ridiculous elements. The game of pass-the-phone stands out as vaguely silly. So too does Scully racing to the rescue, only to wind up at Mulder's apartment to watch a video. And on a pure plot basis, does it make sense that the alien autopsy CCTV would show Zama's PIN number? Or that the Syndicate's First Elder would show up to chat with Scully and let her live? What the Well-Manicured Man unavailable, or is it their plan to reveal themselves to Scully one at a time? (To be fair, there's no indication the Elder knows the WMM reached out to her.) And if that WAS a perfect hybrid in the boxcar, why DIDN'T the Syndicate dispatch a crew to retrieve it? And I've got to say I'm a little miffed the only lead X gives Scully is to investigate her implant. So your big lead is the lead she already had but wasn't pursuing because the script made her forget to? New info: It reads her mind! The point is, mytharc episodes are so much about PLOT (as opposed to other concerns), your audience is bound to notice any and all plot holes.
THE TRUTH IS OUT THERE: Wait. These are human/alien hybrids? What about the hybrids heavily showcased in other episodes, the ones with toxic green blood and superhuman abilities? Well, seeing as the cloned alien visitors also had those features, and the apparently alien Bounty Hunter did too in addition to shape-changing abilities, I'd say there are hybrids created by the aliens, and hybrids created by the humans. The latter have trouble creating viable subjects. Or there are several groups of scientists working on stuff like this, trying to create different sub-races. Zama's group is not Project Purity.
REWATCHABILITY: Medium-High - Important to the mytharc and a good enough thriller, though it's far from perfect, perhaps because the two leads are kept apart almost all the way through.