Standard spoiler disclaimer
[This is the conclusion to my much unanticipated essay on Indoctrination Theory.]
VI Game Over
No matter the choice, the endings of the game vary only slightly. Youtube user Crosscade has compiled a video that juxtaposes six sequences containing what appears to be all the major variations. Most of these, as the video shows, are relatively slight. What’s more troubling about the endings, though, is that they seem to be fiction-breaking oversights on the part of the developer. As Sparky Clarkson writes on Kotaku.com,
No matter what the player chooses, the mass relays detonate spectacularly, releasing massive shockwaves. In the world of the game these relays are the lynchpin of galactic travel and commerce, and their removal separates its the various worlds by voyages that take years, rather than moments. Demolishing the paths of commercial and cultural exchange that defined the galaxy, however, is a minor problem compared to what the game itself states will be the result of the exploding relays.
He then cites the game’s own codex, wherein it states that
Although it has recently been demonstrated that mass relays can be destroyed, a ruptured relay liberates enough energy to ruin any terrestrial world in the relay’s solar system. 
IT sees a loophole in all of this, by explaining that (depending upon the choice), the final animation that Shepard sees is a kind of dream, that plays out in her mind either as part of a reaper attempt to comfort her during her last few moments of sentience, or as some kind of wish-fulfillment fantasy.
It is this part of IT that the more mainstream media seems to have latched on to. In various publications as diverse as gamefront, Kotaku and Forbes.com, writers have commented on the particular “genius” of this ending, all of them convinced that it in some way allows not Shepard, but the player him or herself to experience indoctrination. That is to say, the player’s judgment has been so clouded by the events of the endgame that it is somewhat impossible to tell whether you are making the “correct” choice, and that to do so would involve resisting the game’s attempts to trick you into choosing the wrong side. Most opinions in the mainstream press, too, tend to err ultimately in the direction of skepticism, many of them noting that just weeks after the game’s release, Bioware promised an updated ending that would explain more fully what that final sequence means.
Neither camp, however, can explain in a satisfactory way the meaning of the “destroy” ending, which at this point seems to be the only ending where Shepard may live beyond the final choice. IT implies that in the final moment, that Shepard is awaking on the ground, in London—pointing explicitly to certain objects visible in the rubble that look something like rebar and shattered stone and concrete. Where, precisely, does this leave us? Not in a very good position. Shepard is buried under rubble and gravely wounded. What’s worse, is apparently she never reached the beam, which appears to mean that the battle for earth continues, and that it’s a battle even the united fleets and armies of the galaxy are unlikely to win.
A801506 disagrees with IT’s reading of those final two seconds, and convincingly so. He has taken the video of Shepard’s body lying in the rubble, first brightening the footage and pausing in key locations, then by amplifying the background noise. The brightened footage shows the objects that IT proponents point to as “rebar.” Cutting to scenes from the destruction in London, he shows a number of places where actual rebar is exposed, and it doesn’t look much like the object seen at the end of the game. A801506 then cuts to a number of sequences on the Citadel that demonstrate these objects look considerably more like cables seen during Shepard’s final visit to the Citadel. They appear, in fact, to resemble similar cables seen on the derelict reaper in Mass Effect 2.
Fig. 10. Shepard’s body, as seen in the final seconds of the game. The circle (my addition, for emphasis) indicates the object described as rebar, or as reaper cable. (Source: Bioware Social Network)
Fig 11. Image from the reaper ship in Mass Effect 2. Circle added for emphasis by original poster. (Source: Bioware Social Network)
A801506 points out, too, that the game does not specifically say what materials were used in constructing the Citadel. The in-game codex for Mass Effect is surprisingly silent on the matter, and there is no real way to tell whether stone, concrete, or some other kind of conglomerate might be a key component of the Citadel.
More telling, perhaps, is the amplified audio that A801506 provides. At normal levels it sounds very much like explosions, or collapsing buildings very far away. The louder version demonstrates that there is a distinct, hollow-sounding groan that he claims (and I tend to agree) is usually the kind of sound reserved for surface or space ships, when their hulls begin to collapse and break apart. The use of these particular auditory cues, and the fact that they are somewhat muted, actually fits with the careful attention given to the sound design in the game. Kirk Hamilton at Kotaku.com, for example, was the first to hear a piece of music titled “Vigil” from the original Mass Effect soundtrack emerge from the background noise heard in the war room on the Normandy in Mass Effect 3.
This interpretation leaves Shepard in perhaps an even worse position than the one proposed by IT. The Crucible has possibly fired, the reapers have potentially been destroyed, but Shepard (whom we last saw being enveloped by the blast from the power conduit) is now wounded, trapped underneath a layer of debris, on a space station that is breaking apart, and wearing nothing but a badly damaged hardsuit that can’t be counted on to protect her from the vacuum of space.
Neither of these potential readings necessarily undo the possibility that IT has something important to say about the end of Mass Effect 3. All the same we will need to find a way of understanding IT that includes many of A801506 and his cohort’s observations. There isn’t enough evidence to definitively prove one theory over the other, though what we can say is that there is too much going on within the game, in particular at the end, to dismiss entirely the possibility that something meaningful is happening, even if no one can seem to agree on what that meaningful thing actually is.
In the end, all three Mass Effect games have been about indoctrination in one way or another. On the Feros colony, we even saw something of the battle between organic and mechanical mind control, played out in the conflict between the indoctrinated geth, and the settlers of Zhu’s Hope, who had become thralls of the Thorian. Fai Dan, forgotten in all of this discussion, takes his own life much in the same manner as Saren and the Illusive Man later might. And so if Shepard rejects indoctrination, her decision to do so is an echo of those that have gone before her. Though if you took one of the other two options, well—now what? It’s hard to actually say where the two other endings might lead if IT actually ends up being true, though I doubt that even if those other two endings actually mean that Shepard does succumb to indoctrination, that the “Extended Cut” ending will simply flash the “Critical Mission Failure” screen and ask you whether you want to reload from your last save.
As confusing and upsetting as Mass Effect 3’s ending might have been to the gaming community, the simple fact that it has stimulated debate, and even more importantly close observation of aspects of the game that players generally don’t think about except to complain, is a powerful testament to how much thought the developers have put into what most outsiders consider a generally mindless activity. It’s easy to forget, while in the throes of gameplay that the environments you’re in were built for the player to explore, and even study. And that whatever this new ending may hold in store for us, it’s unlikely that it will fix all the supposed “problems” or answer everyone’s questions. I gather that players will remain disappointed, angry, or confused. Yet some will end up searching for new ways to understand this new ending that are neither entirely what the developers planned, and yet which are not necessarily excluded as potential interpretations of the game. But what’s important to recognize is that IT isn’t a coping strategy for disappointed fans. It’s an earnest attempt to read layered meanings in a game that means much to its players. This in itself has to be some kind of triumph.
 Mass Effect 3 Secondary Codex, “The Reaper War – Desperate Measures.”
 Similar cables can also be found in several of the multiplayer maps, some of which appear as side-missions in single player stories.
 Cf. Kirk Hamilton, “Mass Effect 3’s Musical Secret,” Kotaku.com, http://kotaku.com/5895616/mass-effect-3s-musical-secret, 4/19/2012.