After the Reaper beam hits in London, Shepard's ability to speak, think, and act is significantly and noticeably hampered, and he appears to be physically weak - all of which are known effects of indoctrination. Shepard’s state becomes particularly unusual during his conversation with Starchild, where he doesn't make any attempts to question or challenge Starchild, despite having reliable evidence that many of his suggestions are candidly false, and despite appearing to have a second wind of physical energy.
After the Reaper beam hits, a constant static sound can be heard, occasionally increasing or decreasing to a point of inaudibility, indicating that it may be going into supersonic or infrasonic ranges. Using signal waves like this is a known way for Reapers to condition the mind for indoctrination.
The Reapers have every reason to indoctrinate Shepard. As stated in the Codex: “Should a Reaper subvert a well-placed political or military leader, the resulting chaos can bring down nations.” Also, before beginning the final assault on the beam to the Citadel, EDI notes, “In this battle, the Reapers have no reason not to use their full capabilities to destroy us.” In other words, there’s no reason for them to not try and indoctrinate Shepard.
The word Crucible means "a test or trial of faith/resolve". This could possibly refer to Shepard’s test of will as he fights indoctrination.
After activating the Prothean beacon on Eden Prime in ME1, Liara notes that Shepard has an unusually strong will/mind. This property would allow him to withstand a trial of indoctrination, which would explain why it would take so long for indoctrination to settle.
While on Thessia, Javik explains that their cycle failed because an indoctrinated splinter group tried to control the Reapers. The exact same as the temptation given to The Illusive Man (whose indoctrination is obvious) and to Shepard (the blue option).
In ME1, Saren's ultimate goal is to cultivate the synthesis of organic and inorganic life. This is the exact same as one of the temptations given to Shepard (the green option).
Aboard the Normandy, James Vega complains of a "hum", a known sign of indoctrination. It is not likely to be the mass effect drive-core, as Kasumi noted in Mass Effect 2 that the ship is extremely quiet, adding “I’m not used to hearing my own footsteps.” Considering Kasumi and James were both roughly the same distance from the drive-core, it is unlikely that James would be able to hear it where Kasumi could not. It also seems to be a very deliberate/forced thing to say.
In the cutscene after the explosion, the Normandy crew lands somewhere warm and tropical. When speaking with Garrus prior to the final mission, he says that once the mission is finished, they're "retire someplace warm and tropical." It's possible that Shepard's mind is just seeing what it wants to see, based on recent memories.
While on Thessia, Javik explains that when the Protheans resisted, the Reapers used their own children to betray them. Possible foreshadowing.
Why does the Starchild offer the Destroy option to Shepard? The Starchild seems utterly convinced that the cycle of AI destroying organics will begin again and strongly affirms in a previous scene that it's sole purpose is to prevent this. This was either a lie or it makes absolutely no sense to allow Shepard to pick the destroy option.
Debunked Evidence and Theories
In the Starchild scene, which appears to be exposed to space (like the final fight in ME1), Shepard is not wearing a helmet, and his protective suit appears to be badly damaged. -- This one is partially debunked, and was rather weak to begin with, since it's possible the helmet was removed for artistic reasons, to show Shepard's face more expressively (just like it's possible to always hide squad member helmets during conversations in the options menu). -- From a lore perspective, the Codex also explains that the Citadel wards contain a breathable atmosphere roughly 7 meters high, which is maintained by the rotational gravity simulation and "carefully managed mass effect fields". While the center of the Citadel does not enjoy the luxury of rotational gravity simulation, it is not unreasonable to think that some sort of similar mass effect field technology is being used to contain a small breathable atmosphere. This same technology is seen in the first few minutes of ME2, when Joker is still in the cockpit of the destroyed Normandy.
Adrenaline is thought to speed up the indoctrination process, which further exacerbates Shepard's already vulnerable state after the reaper beam's near-miss. -- Debunked. Adrenaline speeds up the transmission of Dragon's Teeth, the nanites used in the husk conversion process. It does not have any effect on indoctrination.
Trees similar to the ones in your dream are seen after the laser blast. -- These trees are already present before you are knocked unconscious, and are a distinctly different model than the ones used in the dream sequences.
The Star-Child's mesh uses a texture named "Harbinger" -- Confirmed fake.
The piles of bodies in the Keeper Hall and the post-reaper-beam sequence are "poorly textured" and bald. -- A necessity of the engine. Rendering complex, fully textured bodies complete with alpha-masked hair is simply too much work for the engine to handle. There is a reason why we never see more than a handful of enemies on screen at a time. To render a fully-meshed pile of hundreds of dead bodies is simply not possible from a technical standpoint. The easiest alternative is to use fake "mounds" with body textures on it. Typically, a few "feature" body pieces are strewn over these piles, so that your eyes naturally notice the complex "feature" pieces instead of the bland hills.
Bioware/EA has a financial incentive to temporarily withhold a significant portion of the game's content, and has established a reliable modus operandi of doing exactly that over the past 4 years. -- Debunked. The Extended Cut DLC will be free.
Based on the Arrival DLC for ME2, the destruction of the Mass Relays should have resulted in a supernova-scale extinction event in each star system containing a relay, yet people are seen alive. -- While there is still some validity to this statement as it really is not known how the Crucible works, it has been compared to the controlled demolition of a building to the violent destruction of one. It is one thing for a building to be demolished with controlled explosives, and quite another for a building to be destroyed by a giant asteroid. Thus, this point is at least partially debunked based on comparative logic.
In the Control and Synthesis endings, Shepard has the same eyes as TIM and husks. This shows that Shepard has succumbed to indoctrination in these options but not in Destory. -- Though Shepard does indeed appear to have husk-like eyes in these endings, this does not support the theory as the eyes are a result of Reaper technology and not indoctrination. The Illusive Man recieved these eyes after being exposed to Dragon's Teeth (in the Mass Effect: Evolution comic) and not through indoctrination; husks also gain these eyes through the same Reaper device. It should also be noted that if the player plays Shepard as a renegade, a red version of these eyes will become apparant - meaning that Shepard mostly likely had the Reaper technology implanted into him during the Lazarus Project in Mass Effect 2.
Responses to Counter-Arguments and Other Questions
If the red ending is the correct choice, why is it the easiest choice to unlock? Shouldn't it be the hardest? -- The face-value answer to your question is that the more time you spend building an army, the more time the Reapers have to slowly prepare you for indoctrination. This is in line with the same timing elements used in the ending of ME2, where spending too much time doing sidequests and loyalty quests after a certain point led to detrimental results for the Normandy crew. -- Finally, from a psychological standpoint, Bioware wants the red option to feel wrong, like it's the worst choice. That's part of the "indoctrinate the player, not just Shepard" plan - if ever such a plan existed. By making the other two choices harder to unlock, it makes the red option seem even worse. There's also a much more practical position to consider: If the red option is going to be the 'correct' choice in future content everybody will have to be able to access it. Player backlash would be enourmous if they couldn't unlock the canon choice easily.
If choosing the red option would allow Shepard to break free from indoctrination, why would it even be offered? -- While it is the only choice that allows Shepard to break free of indoctrination, it is also the only one that can have repercussions for Shepard, depending on your EMS. Choosing the red option can still mean succumbing to indoctrination, which is represented by the destruction of Earth. Also it is important to keep in mind that the whole scene with the starchild is a representation of Shepards psyche in the context of IT. The Destroy option is the part of Shepards mind struggling against the indoctrination attempts by the reapers. The presence of the red option is much much more non-sencial outside of the scope of Indoctrination Theory (see above).
If Shepard is indoctrinated, why doesn't the VI on Thessia detect it? -- This is a tough one to tackle, because we really just don't know much about how a VI detects indoctrination. -- First, we're assuming that the VI is even talking about Kai Leng. It states that indoctrinated presence is detected while Shepard is still present. Granted, it does not say this until Kai Leng walks up and after a short conversation with Shepard, but anything is a possibility. -- The most common and simple response to this argument is simply that Shepard is either not indoctrinated until Harbinger weakens and mentally attacks him on London, or that he is not indoctrinated enough for the VI to detect it.
Shepard's indoctrination appears to have taken a very little amount of time, if we assume he was not indoctrinated when speaking to the VI on Thessia. -- The codex explains that "rapid indoctrination is possible, but causes this decay in days or weeks." Bear in mind that it is not the rapid indoctrination that takes days or weeks: it is the decaying effects of that indoctrination: physical weakness and loss of higher mental capacity. Harbinger is one of the largest and most powerful Reapers we know of. It is not unreasonable to assume that his indoctrination abilities are powerful enough to attempt rapid indoctrination with Shepard, especially in his physically weakened, unconscious state. He isn't necessarily concerned with the long-term use of Shepard: he only needs to indoctrinate him long enough to create a few critical mistakes, harnessing Shepard's position of influence among the allied fleets. However, considering the large amount of contact Shepard has had with Reapers and their technology, it is not unlikely that indoctrination started much earlier but did not surface until the end.
If Harbinger is able to attempt rapid indoctrination on Shepard, why wouldn't he have done it much earlier? -- It's plausible that he has already made attempts: such as the vision of the child on Earth, or the dreams after each Priority phase. Indoctrination works best on a target that is weakened, physically and cognitively. Attempting to rapidly indoctrinate Shepard when he is at a normal physical and cognitive capacity may have provided less of an opportunity, and Shepard's strong will was able to resist. -- Additionally, Harbinger has an incentive to let Shepard build an allied army before indoctrinating him. The more influence and authority Shepard has when he is indoctrinated, the more Harbinger can accomplish by using him before the mental and physical decay of rapid indoctrination make Shepard useless as a tool. -- Finally, it's plausible that physical proximity empowers the effects of indoctrination, and Harbinger simply hasn't even been in such close range of Shepard. We see him easily controlling the Collector General from the depths of dark space in ME2, but the Collector General is the mindless husk of a Prothean, reaper technology, which Harbinger could indoctrinate far more easily. It's also entirely that because the husks are reaper technology, the ability to assume direct control is not related to indoctrination in any way.
Indoctrination is not something you simply break free of. The only examples we've ever encountered of resisting indoctrination are temporary moments of sanity made by incredibly strong-willed people (Saren, Benezia) on the brink of death. -- Correct, Shepard is an incredibly strong-willed person and at the brink of death. Thus he is resisting indoctrination. -- To continue on this, however, we know of at least one confirmed case of an organic reversing the effects of indoctrination: Shiala. She fell under Sovereign's indoctrination, but was traded to the Thorian in exchange for knowledge of the Cipher. It is not clearly explained how, but Sovereign's indoctrination was supplanted by the Thorian's unique control mechanism (which bears a lot of similarities and serves as a useful, if not perfectly transferable, analogue to indoctrination). When the Thorian was killed, Shiala was set free of its control, leaving her in charge of her own actions. In fact, Shiala and the other released thralls on Feros were able to use the remaining traces of the Thorian's "indoctrination" to enhance their own communications, turning a ragtag group of militia into a powerful military force capable of fighting against the Reaper threat. Shiala seems to acknowledge that there are still traces of her indoctrination present, as she can feel the Reapers' influence in her mind, but that she is able to wholly resist these influences because of her Thorian-given connection to the other colonists. -- We also know of at least one case of an organic being resisting Reaper indoctrination with almost perfect results: the Rachni Queen. We know that it is not simply a biological immunity, as her spawn as easily indoctrinated by the Reapers, and other queens appear to have been indoctrinated during the Rachni Wars. But for unexplained reasons (presumably, the tremendous amount of mental fortitude required to manage a hivemind), this particular Rachni Queen resisted Reaper indoctrinate so perfectly that the Reapers resorted to physical restraints.
The game's ending text message tells you that Shepard has thwarted the Reaper threat. If the Indoctrination Theory is true, this text message is false. -- It is likely that this message, like the Stargazer scene, was included by Bioware to reinforce the illusion that we were given a finished product, in order to thwart the inevitable outcry over selling an incomplete game once the free Extended Cut DLC is released.
In the "perfect" ending, it is not clear that Shepard is actually in London. It's possible he is inside the wreckage of the Citadel. -- If the assumption that the rocky rubble is not London is false, then we no longer need to explain the atmospheric re-entry problem. However, we're still faced with the child lying, and with Shepard surviving the explosive destruction of the citadel, which I assume would also have disrupted its simulated gravity rotation. Also, the Citadel does not appear to be constructed with any rocks/stone in any location.
An order to fall back was given as Shepard was waking up. It's possible that the Normandy evacuated Shepard's squad, but couldn't find his body, and left without him, making a beeline for the nearest relay, which explains how the squadmates "teleported". -- First, it is somewhat unusual to believe that the Normandy would participate in this retreat, given that the order was given by a ground team commander over ground team radio, not by Admiral Hackett - and given that several other ships are seen fighting in orbit while Shepard is talking with the Starchild. It also ignores Joker's previous behavior, risking life and limb for the mission. Even discounting all of these things, the Normandy would have only had about 20 minutes to make it from Earth to the relay.
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