There are major spoilers for Star Trek Into Darkness within.
It’s hard to find much by way of coherent themes or meanings in Star Trek Into Darkness, one of the most ineptly written blockbusters of an era when ‘inept’ is seemingly the goal. Little in the movie makes logical sense, either taken as a whole or taken scene to scene (Kirk making Chekov the chief engineer, Khan hiding his friends in torpedoes he knows will be used, Admiral Marcus assuming Kirk will shoot 72 torpedoes at one guy, etc). But under it all lurks a movie - perhaps a half-realized one - that is a metaphor for the Truther views of 9/11.
Those views didn’t get there by themselves; co-writer Bob Orci is a huge conspiracy theorist. So huge, in fact, that on his (now deleted) Twitter he calls rational people “coincidence theorists.” As in, “Oh, so you think it’s a coincidence that the fire department commander said they were going to ‘pull it’ just before World Trade Center Building 7 collapsed, despite it having never been hit by a plane?” Orci has in the past taken to his Twitter account to ‘ask questions’ about the official story of the attacks on 9/11, as he fancies himself some sort of free-thinker - free of an understanding of physics, politics or reality, one assumes. Those Truther views - that the attacks on the Pentagon and the World Trade Center were inside jobs perpetrated by those in power in order to attack unsuspecting countries - have made their way into the film.
First, a look at the facts of the case, or what happens in Star Trek Into Darkness:
Admiral Marcus’ secret deep space exploration program finds the SS Botany Bay. He thaws out Khan. Marcus, in the aftermath of the destruction of Vulcan, is feeling very security-minded, and he thinks war with the Klingons is inevitable. He enlists the thawed out, centuries-old dictator Khan - for reasons that cannot be explained by the film or logic - to build advanced torpedoes and space ships so that the Federation can have an edge on the Klingon Empire.
His bargaining chip is the Botany Bay’s full complement, the 72 men and women still frozen. Khan, the superman, is in Marcus’ thrall while the Admiral has them. Khan’s plan is to build the advanced torpedoes and then hide his people in them, a plot that makes so little rational sense as to perhaps be brilliant. Anyway, it doesn’t work and Khan thinks his crew has been killed, so he starts a vengeance campaign that makes almost as little sense as his torpedo brainstorm.
He convinces a Starfleet officer to suicide bomb what seems to be just a records depot, but what is actually a secret base for Section 31, Starfleet’s black ops division. That attack triggers an automatic meeting of all local ship captains (and their first officers, so that the Kirk and Spock characters can be there), which was Khan’s plan all along. He wanted to get all these folks in one place and then kill them, which he tries to do by emulating the helicopter attack scene from The Godfather Part III (which he could have seen in theaters, going by the original timeline that has the Eugenics Wars starting in 1992). When he fails to kill anybody except for Christopher Pike, who he doesn’t even know, Khan transports himself to the Klingon homeworld.
Which is an extraordinarily dumb move, as he knows that Admiral Marcus is dying to start a war with the Klingons. Tracing the beaming route of a known terrorist (he was identified after the first attack, possibly in a message sent directly to the Admiral by the reluctant bomber) to the Klingon homeworld would certainly give Marcus plenty of ammunition to launch a pre-emptive attack, one which would be focused on hunting said terrorist down. In fact, the only reason someone of Khan’s superior intellect would ever do something like that is… if it was the plan all along.
Truthers say that the attacks on the World Trade Center and the Pentagon were false flag incidents; a false flag attack is a secret military operation executed under another nation or group’s flag, to make it seem like someone else was responsible for it. The theory that Truthers have is that the US government actually attacked the United States and pretended to be Al Qaeda to do so. The murder of 3000 Americans was to give the US an excuse to invade oil-rich countries in the Middle East.
As poorly explained onscreen in Star Trek Into Darkness the terrorist attacks aren’t false flags, rather they’re what is known as blowback - where a nation undertaking a covert op suffers some consequence as a result of that op's success. It could be argued that 9/11 was actually a case of blowback, as CIA funding and training of anti-Soviet Afghan mujahideen may have laid the groundwork for Al Qaeda and their abilities to strike the United States. In the movie Khan’s attacks are blowback from Marcus’ secret preparations for war (and Khan's final act, crashing the Vengeance into San Francisco and killing likely hundreds of thousands of people, is direct blowback from Spock tricking him into thinking the 72 detonated torpedoes carried his crew).
But none of this makes any sense in the context of the film. Why would Khan attack Section 31, which requires him to go through the effort of recruiting an officer to act as a suicide bomber? He could have caused the same fleet meeting to be convened by hitting an easier target. And why would he possibly beam himself to Qo’nos, the one place in the galaxy the guy he hates most wants to attack?
Things look different if we put on our Bob Orci conspiracy hats and stop acting like sheeple. After all, the bomber sending a message to Marcus - what’s that all about? Perhaps that’s part of the plan, a notice to the true ringmaster, giving him a heads up. Destroying Section 31 allows Marcus to cover his tracks; the Vengeance, his supership, is pretty much already built, so it makes sense to clean up the evidence of what Khan was doing. In fact, if Khan wanted vengeance on Marcus the last thing he would want to do would be to blow up the place that proves Marcus’ involvement in potentially criminal plots.
By the way, Section 31 is hidden in what appears to be a regular office building that also contains a very boring governmental facility, an archive in this case. World Trade Center 7, the building that Truthers believe was ‘pulled,’ housed an administrative CIA office on the 25th floor. Truthers claim that WTC 7 was destroyed in order to cover the tracks of those who orchestrated the 9/11 attacks, tracks that could have started in that CIA office, just as Khan's tracks would have started at Section 31.
Khan’s attack on the Starfleet meeting also makes little sense. He’s hovering in a jumpship, firing hundreds of rounds into a small conference room and seems unable to actually kill just about anybody. It’s plausible that Khan could have taken out the fleet’s top captains in seconds; instead Pike seems to be the only notable casualty. But what if Khan didn’t want to kill anyone? What if the attack was intended just to put Starfleet on a war footing? What if most of those captains were meant to survive so they could wage war on the Klingons?
Such an attack doing so very little damage reflects the most extreme Truther claims about the attack on the Pentagon, namely that it was a missile that hit the seat of military power, as a passenger plane would have caused much more damage to the structure. The argument here would be that the attack on the Pentagon was never intended to really destroy the building, but rather to punch the military in the nose just hard enough to whip it into a fighting frenzy. Which would be exactly what Admiral Marcus wanted to do.
Finally Khan transports to Qo’nos, leaving behind the transporter device - which actually has his destination coordinates on display. It’s a direct line to the Klingons, allowing Marcus to show the Federation who was truly behind the attacks. After all, why else would a human escape to the Klingon homeworld? This reflects the fact that the passport of hijacker Satam Al Suqami was recovered immediately after his plane slammed into the World Trade Center; for Truthers this ‘miraculously intact’ passport is evidence that the government was framing Middle Easterners in order to launch a war effort.
Later in the movie it’s revealed that Marcus actually IS using Khan’s attacks as a way to start a war, but in the dumbest way possible. Rather than use Khan’s travel to Klingon as a pretense to attack, he sends the Enterprise on a dopey assassination mission and then sabotages their warp core so they’ll be stuck near Klingon space. He assumes that Kirk will rain 72 missiles onto Qo’nos, killing Khan and erasing his crew, and then be trapped when the Klingons show up to investigate - basically it’s Star Trek’s version of the Gulf of Tonkin, the incident which gave the US an excuse to go to war in Viet Nam. As presented in the movie it’s mostly a spur of the moment thing, like Marcus is taking advantage of Khan’s ‘defection’ in order to jumpstart his war. Like so much else in the film that makes no sense, especially when you take into account that all of this occurs on the day when he happens to be launching his new super-secret supership (which is the movie's stand-in for drone warfare, but that’s part of the overarching stupidity. Why you’d build a ship that big if you didn’t need to have a lot of people on it is beyond me).
Khan himself maps to Osama bin Laden. He’s a fierce warrior and leader who works for Starfleet (or with the CIA in the 80s) before he becomes a patsy/rebels against his masters (whichever version of the 9/11 conspiracy stories you believe). He’s a man out of time because there’s a popular Western notion that Al Qaeda is made up of people living one step out of the Stone Age, that the mujahideen are essentially regressive savages. It’s that savage quality that Khan says makes him valuable to Marcus.
Oh, and by the way: there are 72 torpedoes holding 72 of Khan’s crew. If that number is familiar to you it’s because that’s the number of virgins we’re told jihadists will get in heaven after they martyr themselves for Allah. Bob Orci didn’t arrive on that number on his own - in the original series episode Space Seed the SS Botany Bay’s crew of 84 has been reduced to Khan and 72 others by the time the penal ship is found - but it is something of a gift to him.
Orci didn’t write the film alone; regular co-writer Alex Kurtzman and Damon Lindelof also get credits. And the film doesn’t hide its political bent - it is dedicated to vets, and not just any veterans. The dedication is:
THIS FILM IS DEDICATED TO OUR POST-9/11 VETERANS
WITH GRATITUDE FOR THEIR INSPIRED SERVICE ABROAD
AND CONTINUED LEADERSHIP AT HOME.
There are even some real-life Iraq/Afghanistan vets in the movie, playing background roles. Clearly the film is saying that these brave vets fought in wars that were started without the best interests of Americans at heart - there is simply no other way to read the politics of the film. But the finished movie stops just shy of endorsing the idea that the terrorist attacks that got us into these two wars were, in fact, perpetrated by our own government as part of a terrifying and complex scheme.
Still, it’s there. Just under the surface. And it’s so cynical that it seems to spit in the face of everything Gene Roddenberry wanted Star Trek to be. There have been iterations of Star Trek - most notably Deep Space 9 - that explored the grey areas of what it means to be a non-militarized peacekeeping group, but that exploration happens at arm’s length from the original series that carries Roddenberry’s stamp. Roddenberry’s future had imperfect humans striving to be better and to fulfill lofty goals like working together, finding commonality with all sentient life, and bringing peace and happiness to every corner of the galaxy. That galaxy reflected the then-modern political climate, with the Federation/Klingon tensions mirroring the Cold War, but it was always seen through Roddenberry’s essential optimism. It was also always seen through Roddenberry’s essential humanism - every side of every conflict had a reason for their actions.
Star Trek Into Darkness has a more venal view of humanity. At best Admiral Marcus is willing to put one of history’s worst tyrants to work in order to facilitate a war he plans to start (by killing everyone on the Enterprise); at worst Marcus uses that tyrant to murder innocent people in order to start that war (and he also wants to kill everyone on the Enterprise). While there have been Starfleet officials who have been bad guys in the previous Trek continuity, Marcus is special because he’s the very head of Starfleet. In the reboot universe Starfleet isn’t dealing with occasional bad apples, it’s rotten from the very top. It is an organization run by criminals, something that would not have fit in Roddenberry’s vision.
I find Truther beliefs to be among the most distasteful possible, and to have even a whiff of them in Star Trek troubles me deeply. The fact that, like every other part of the script, they’re botched and barely work doesn’t make it any better.