Having covered my general thoughts on the film and its broad connections to the mythology, I will now elaborate on some of my disappointments and explore some of the aspects that I think were successful.
Apparently the film was cut for length, and I can't help but wonder if the excised footage, once restored, will have the same effect that I've seen with other films that have suffered in the theatre. A lot of studios are taking a jaded approach to initial release: they cut for time, cut to get a PG-13 rating, all designed to maximize theatre earnings (at least in their own mind). The "real" film is later released on DVD, where the restoration drives sales and additional profit.
The audience has become savvy to this methodology, and a lot of people refuse to see certain films in the theatre, because they want to see the complete version of the story when the DVD arrives. Yet the studio continues to use the box office as a measure of success. It's akin to using Neilsen ratings for television in the era of season-set DVDs, Netflix, legal digital downloads, and everyday DVR recording.
I now have to wonder if the elements I felt were missing were simply cut for time. If so, I think it was unfortunate, and it may merit a closer look should a longer version arrive on DVD. (Early indications are that the Blu-Ray version of the film will have an entire buried traincar of extras.) Most of my annoyances were related to character and context, specifically the lack of background on the changes to Mulder and Scully's lives after "The Truth". As I said in the general commentary, it wouldn't have taken much time at all to include that information, so if there's a lot of footage on the cutting room floor, it might have been there.
At the beginning of the film, it is revealed that Scully is now working as a doctor at a Catholic hospice, dealing with unusual cases and applying her broad expertise. She claims not to be working with Mulder anymore, but he is either living with her at a secret location or living in secret in a nearby home (it wasn't entirely clear to me what their arrangement was). Mulder was effectively a recluse, hanging out in a mostly empty house, sitting in an office made up to look like his old basement demesnes.
This is a fairly significant turn of events as compared to the end of the series. "The Truth" had both Mulder and Scully on the run from an FBI (and federal government) overtaken by apparent alien super-soldiers. Mulder was in the midst of his crusade to uncover the truth about the 2012 "colonization" plan, and Scully (along with Agents Doggett, Reyes, and Skinner) were directly implicated in Mulder's eventual rescue and survival.
The point is simply this: Mulder is not the only one who would have been a fugitive from the FBI. It was not simply that he was wanted for murder. It seems almost impossible that he would be left alone for six years, and even less likely that he would go from an active crusade against "colonization" to a man sitting around cutting out newspaper articles. Considering how easy it should have been to find Mulder if he was anywhere near Scully, one can only conclude that the FBI (and the "aliens" controlling the FBI) was willing to let him rot…despite every indication during seasons 8 and 9 that this was not their position.
Oddly enough, it's Scully's public life that is more puzzling. One might accept the idea that Mulder was forced to ground, but he was last seen with Scully in tow. The end of the series strongly implied that she was just as much on the run as Mulder. For her to be living a relatively comfortable life just doesn't fit, and that's one item that the writers completely ignored. Yes, it makes sense that a free and clear Scully would step back into her medical career (as was often threatened during the series), but she wasn't free and clear.
The exact relationship between Mulder and Scully is also rather muddled. The series pointed to a future together, but they often seem out of touch with each other throughout the film. At the same time, they are obviously lovers, and more open than one would expect them to be if they were mostly apart for six years. One could just say "it's complicated", but we already knew that from the series.
While a number of people view the relationship between Mulder and Scully with glowing praise, it’s actually quite disturbing. Their relationship brings a new meaning to the word “co-dependence”. Mulder’s obsessive psychology makes Scully an almost necessary part of his thought process (to the point where it drives him insane when she’s not around), which only serves to make any absence of her from his life for any length of time hard to reconcile.
Scully, on the other hand, has a fascination with men in authority over her life, which is in stark contrast to the strength she otherwise conveys. Mulder's rebellious nature appeals to her on a fundamental level, and she was willing to stay with him as everything and everyone from her previous life was slowly but surely torn away. By the end of the series, for better or worse, Scully has nothing left but Mulder, just as she remains Mulder's last shred of support and sanity.
None of that is readily apparent in this film, and there's no attempt to bridge the gap. And it's not necessarily easy to recognize that problem, because the earliest scenes in the film gloss over the depth and complexity of Mulder's "fugitive" status. Agent Whitney inadvertently sets up the plot for failure when she indicates that if Mulder comes to help, "all is forgiven". Never mind that an "alien"-controlled FBI wouldn't be so easily swayed, but does the nature of this particular case really equate to Mulder's apparent legal status?
It also doesn't seem to make sense for Agent Whitney to call on Mulder's perspective at all, especially not in terms of his background in the paranormal. It's hard to imagine that this is the first case in six years to involve something unexplained, given how often "normal" agents ran into problems during the course of the series. One might wonder if Cancer Man is working through a protege again, since no explanation is ever given for why Agent Whitney would have been interested in the X-Files or Mulder's tenure.
The policy on Mulder at the FBI, and the ignored joint fugitive status of Mulder and Scully, all pertains to Walter Skinner as well. It's great to see an old familiar face, but Skinner was last seen in the clutches of the conspiracy at the heart of the FBI. He shows up in this film without the slightest indication of how he survived, how he managed to remain in the Bureau, or how he could possibly still be in a position to help Mulder and Scully. Of all the characters in need of a little more background, Skinner probably would have been the most difficult to manage.
It's not as if it would have been difficult to come up with another reason to pull Mulder and Scully back into a case together. Mulder might have been contacted to evaluate Father Joe based on his superior profiling skills, which were often cited during the series and was one major reason for his original good reputation in the Bureau. This, in turn, could have helped to give more weight to Father Joe's inclusion and the questions surrounding his "visions".
Bringing Scully into the mix could have then provided a means of exploring, in rather short order, the status of their relationship over the past six years and where they presently stand. The end result could have been exactly what we see in the film, but it could have made Mulder's presence more logical and it would have provided a better context for their crisis later in the film.
That crisis is predicated on the idea that Scully has been away from investigating the macabre and paranormal for long enough to reject, on some level, Mulder's return to his crusade and the darkness it brings. Because the context of their relationship was murky at best, I didn't quite buy Scully's reluctance, especially in light of what she had sacrificed in service to Mulder's crusade and her eventual decision to join it.
If Scully's patient was meant to stand as a reminder of William, and therefore a trigger for Scully to re-evaluate her role as Mulder's steadfast fellow crusader, it wasn't given enough attention. Scully would routinely question the cost of her devotion to Mulder during the series, and it was almost always tied to something she had lost or was about to lose. If it was transference, then why wouldn't Mulder confront her on that more? Given that Scully knows Mulder inside and out, it's odd to consider any situation where she would wonder over his motives and responses.
But on some level, there needs to be conflict somewhere, and tension between Mulder and Scully is usually where it ends up happening. I thought the writers did a nice job of forcing Scully into some tough emotional territory, especially if her patient was meant as more than the indirect source of a coincidental discovery of illegal transplant research. She could tell that the universe was giving her a message, and she wasn't particularly pleased with the details.
It would have been better if her time at the religious crossroads was more apparent. Scully clearly has an issue with the notion that anything God-like might be using a pedophile priest as a means of revelation. It definitely doesn't sit any better with her when it becomes more and more likely that Father Joe is being offered a chance at redemption for past sins.
The stem cell research angle seems to promise that Scully's ideals of faith will be tested by the use of a treatment that is in contradiction to Church doctrine. Her initial conflicts with Father Ybarra also seem designed to culminate in a battle over those procedures. It would have been a lot more interesting (and meaningful) if Scully had come to the realization that doing the right thing for her patient and saving his life meant taking an action that was as questionable and unethical in the eyes of her faith as Father Joe's transgressions. That's exactly the kind of role Father Ybarra could have played.
That conflict is implied, just as it is implied that it feeds into her disagreement with Mulder. Scully questions the nature of the source of Father Joe's visions, especially when they seem to be driving her to use the stem cell therapy. But it's never entirely clear how all of those conflicts and psychological issues fit together or why she finds resolution. We're not even privy to the fate of her patient! (Though, to be fair, the moment in the end credits would seem to imply things ended well.)
If one manages to assume that all of those psychological factors are at work with Scully, then it would be a good extension of what was seen on the series. Mulder, on the other hand, barely gets a shred of character development at all. Mulder is, for all intent purposes, Mulder. The only shocking concept for Mulder in the film is the notion that he might have been sitting around doing nothing for six years!
This is where Mulder's profiling skills would have benefited the plot. Let's suppose that Mulder is brought in to evaluate Father Joe as a profiler, and initially, he doesn't believe but he thinks Father Joe has the answers. What if he began, over time, to believe in Father Joe, becoming more and more overt and demanding in that belief? Had it then been established that Mulder had chosen to avoid X-Files-esque work for six years, and that this was a restoration of his belief, it would have made more sense.
Instead, the writers try to connect the abduction of two female victims to Samantha, and it just doesn't hold water. While Mulder is never going to get over Samantha's abduction and eventual "death", he had more or less come to terms with it. There was nothing in the current situation to bring up those old feelings. Worse, it felt like a holdover from the original version of the story, which was supposedly set during the fifth or sixth season. Using Samantha as a "living" motivator then would have made contextual sense; six years after "The Truth", not so much.
A couple other issues also came to mind. While I understand that some fans were unable to warm up to Agents Doggett and Reyes, it would have been nice to get some insight on their fate. To be honest, the roles filled by Agents Whitney and Drummy would have been ideal for Reyes and Doggett, respectively. On the other hand, Robert Patrick and Annabeth Gish would have been hard to cast, given current obligations, and if the writers couldn't work in context for Mulder and Scully, they certainly couldn't have done it for Doggett and Reyes!
I was also a bit bothered by some aspects of the case itself. In essence, one gay man was kidnapping and murdering young, athletic women so he could provide his husband with a new and healthy body. Was there any particular reason to make the "monsters" in this film a homosexual couple? And why in the world would a gay man choose to give his gay lover the body of a young woman? I understand the value of making the recipient one of Father Joe's young victims, but wouldn't it have made more sense for the killer to kidnap young athletic men, in that case? As it stands, it looks like another example of using the torture of young attractive women for entertainment, which is unnecessary.
Hopefully this gives some additional insight into why I thought the character exploration and context was lacking in this film. To be honest, this is simply what gathered in my mind after one viewing of the film. It's possible that my perceptions would change if I saw the film again, but I honestly doubt it. The issues were built into the elements of the film, and some of those issues simply cannot be repaired. Some, however, might be the result of the deep cuts made to the film before theatrical release. It remains to be seen if a "director's cut" of the film emerged, and if so, what mysteries might be resolved as a result.
