The index to the entire Joss Whedon roundtable is here.
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One of the main strengths I’ve recognized throughout Joss Whedon’s work is his careful crafting of deep, multifaceted characters. He puts enough care and attention into them to ensure they aren’t simple cardboard cut-outs that drive the story along, but persons whose reasoning we can understand. In addition to his complex characters, Whedon focuses on the concept of the family. It’s a recurring theme that, however alienated the characters are when introduced, they’ll inevitably will be drawn into a tight familial group. Case in point, the Scooby gang in Buffy, the crew of the Serenity in Firefly, Angel investigations crew in Angel, the Los Angeles Dollhouse or even, to a lesser extent, the Avengers.

A striking point in Whedon’s work is that these familial groups eventually confront militaristic organizations in one form or another. Some of these organization appear as a benevolent force at first and turn into a tyrannical opponent afterwards, such as the Initiative in Buffy the Vampire Slayer. Some are conventional “villains” from the onset, such as the Alliance in Firefly or the facility operators in Cabin in the Woods. All military industrial organizations we see in Whedon’s work have a clear path: self-destruction. This trajectory is present throughout Whedon’s work; as the military acquires knowledge of powerful artifacts (or powerful persons depending on the genre) they try to weaponize it. Despite the best of intentions at times, the moment the military tries to harness these “powers, they’re propelled onto a collision course with our protagonists. It’s a matter of arrogance; the military sees the potential for power in something and assumes that they are strong and righteous enough to control it, but are ultimately consumed by it. The characters we follow are no less tempted by this thirst for power, but aren’t as misguided by hubris and only resort to wield the artifacts in question as a last resort to avert disaster. In the rare cases where our protagonists yield to those temptations, their punishment is swift and their remorse keeps them from following the military down an ethical slippery slope. This recurring narrative shows a distaste for the hubris of the military organizations and sows the seeds of anti-authoritarian thoughts, but there may be more to it than this.
 

 
I wonder if this relationship between his characters and the organizations around them is a reflection of a long running theme of anti-authoritarianism or perhaps, a reflection of Whedon’s troubled relationship with the studios he has worked for. For decades, his battles with studio executives have become well-known and documented. Angel was cancelled over posturing, Firefly was doomed from the start, the networks backed out of the Dollhouse premise and his recent comments about the Marvel Studios fiasco seems to only hint at the contentions between them. As the subtext seeps into the plot, his complicated and tense relationship with his employers is difficult for the audience to ignore. It’s hard to know which came first: is the underlying anti-authoritarian theme the result of studio conflict, or do the studios rush to stifle Whedon’s creativity when it starts to veer towards difficult themes? Whatever the case, this theme is growing more pronounced with every new piece that Whedon produces.

Buffy developed a huge fan following due to the care and attention Whedon put into building an intricate world and multifaceted characters. The studios want to capitalize on this success and rake in the profits, but balk at the time it takes to build the story. They jump at the idea of working with Whedon, giving him some freedom at first, but become increasingly intrusive and controlling, as they have a very strict idea of where and how the story should be told. They call a halt when Whedon veers off the “acceptable” course or takes too long to get somewhere, and this window is getting narrower the longer their partnership lasts. The studios, much like the military organizations, don’t understand what they have and try to exploit it. They try to capitalize on Whedon’s strengths without understanding them for their own purposes (profit, brand recognition) but it is not what Whedon seems to want to do, which is art.

Is Whedon’s negative relationship with the studios the only thing that affects his writing?
Whedon also seems to enjoy working with regular artists and contributors over time and, although this interaction is normal, it reinforces the subtext. Close friends and the family you create are better and stronger than the organizations you associate with, (corporations and the military industrial complex included). Those entities are bound to destroy themselves through their own misdoings and hubris.

These musings bring the slaughter of the white collar drones and the military organization in Cabin in the Woods into a new light. The military may want to do well, but trampling the civilians and treating them as expendable causes their downfall. The small group of survivors, whether considering this movie or Whedon and his close creative partners, band together and fight back, no matter the cost. They lose their life for their freedom in the former; Whedon loses his job for his freedom in the latter.