Indoctrination Theory.

This thread is a
vitalization and continuation of an Indoctrination Theory thread started
on the BSN (Bioware Social Network) by community member Byne.

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Key Theories of Indoctrination
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Harbinger's Attack Theory

This
theory roots itself in the beginning of Hammer Squad's run towards the
Citadel Conduit, when Harbinger is trying to destroy the squad and
protect the Conduit. Shepard is knocked unconscious when the laser beam
narrowly misses but wounds the Commander.

The basis is that while
Shepard is lying unconscious on the battlefield, they are hallucinating
getting up and making it to through the beam and up onto the Citadel.

This is the most strongly supported theory by in-game evidence and the strongest explanation for the endings.
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Elevator Theory

This theory roots itself in the scene after both Anderson and Illusive Man die in the control panel room.

The
basis is that Shepard does indeed wake up and make it through the
Conduit, reaching the control panel room with a final showdown involving
Anderson and Illusive Man. Bleeding to death, Shepard tries to reach
the console again to activate the Crucible but faints and is lifted by
an elevator to the exterior of the Citadel to meet Catalyst.

There is some strong supporting evidence for this theory but also strong evidence that disproves it.
---
Illos Run Theory (developed by Byne)

This
theory roots itself in the beginning of the final push against the
Reapers on Earth in London, during the scene where the Hades Canon must
be taken out by Shepard's squad. Cortez's Kodiak is shot down shortly
after dropping Shepard off. The scene bears some resemblance to the
Illos level of Mass Effect when trying to reach the Conduit.

The
basis is that the Kodiak was shot down before Shepard could disembark
and Shepard is lying under rubble, hallucinating the whole scene from
the Hades Canon onwards.

This is probably the weakest of the
three 'main' theories behind indoctrination because there is not a lot
of supporting evidence behind it.

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Key Evidence
This is all IN-GAME evidence that has been analyzed by the community to support (or debunk) the viability of Indoctrination.
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Meeting Catalyst
This
is one of the most controversial scenes in the Mass Effect 3 ending.
There are many things that can be taken from this scene alone that help
support Indoctrination.

First is the location of
the connection point between the Crucible and the Citadel Tower. This is
where the elevator takes Shepard and 1-3 'choices' are presented. The
central beam is the connection point between the Crucible and the
Citadel Tower. There is a large 'error' with this scene.

Shepard is standing in the total vacuum of space without a proper environment suit or helmet.

This image, provided by
ceruleancrescent (I think), depicts the docking point of the Crucible to
the Citadel. The white arrow is the direction of the Citadel Tower, the
Crucible is docked at the base. The green and red circles are where the
Crucible beam connects with the chasm into the base of the tower. The
yellow circle is the approximate area of the partial tunnel Shepard
walks down. The two blue arrows indicate the front and back of the
Citadel Tower. Some have argued that Mass Effect fields created by the
Citadel create an atmosphere in that area, but the only areas on the
Citadel with an atmosphere are the Wards.

Citadel Wiki Entry on the Wards

The
"arms" of the Citadel, known as the Wards, constitute the residential
and commercial sectors of the station. Densely populated, housing
millions of residents from many galactic species, the Wards are akin to
Earth cities such as Hong Kong and Singapore. Numerous skyscrapers rise
from the superstructure, sealed against vacuum, as breathable atmosphere is only maintained to a height of approximately 7 meters.
Unlike the Presidium, there is no artificial day-night cycle; as a
consequence of this, commercial activity rarely ceases, and residents
work and rest according to personal need. Barla Von appropriately dubs
the area the cultural heart of the Citadel, and therefore of Citadel
space. The Wards are policed by the Citadel Security Services (C-Sec),
whose offices and custody suites are located in the Lower Wards. Flux is
a popular night club, also located in the Wards.

There are several other
key points with this scene that will be summarized and gone into depth
in other threads or in later posts in this thread.

• 
  If Shepard reaches this point with a Low EMS, Catalyst will only
  present a single option to Shepard; Destroy (Destroyed Collector Base)
  or Control (Collector Base Intact).
  
• If Shepard's EMS score
  is in the 3200 and up range, all 3 choices should be open. Catalyst will
  describe Destroy as the worst option and Synthesis as the best option.
  
• 
  Destroy and Control are colored in the Paragon/Renegade scheme, yet
  Anderson is shown on the Destroy option and Illusive Man on the Control
  option, which is a reversal of the Paragon/Renegade scheme.
  
• Catalyst is in the form of the young boy Shepard sees in Vancouver in the beginning.
  
• Shepard is very 'out of character' and does not show any initiative to question Catalyst's words.
  
  
  
  
  Crucible Control Panel
  
  
  
  
  
  This scene takes place
  before the meeting with Catalyst. Both Anderson and Illusive Man are
  encountered here for one last conversation before the end of the game.
  There are also several 'errors' with this scene as well as one large
  clue.
  
  
  
  
  
  
  During points in Illusive
  Man's speech, 'oily shadows' will appear on the edges of the screen,
  often accompanied by a deep, vibrating sound that is associated with the
  Reapers. This strange edging has been mentioned by the Rachni Queen,
  who perceives sound differently from other organics, since it serves as a
  form of sight and communication for her species. She mentions the 'oily
  shadows' the Reapers create when trying to indoctrinate her and and her
  children.
  
  During this entire scene, Anderson and Illusive Man
  seem to take on the roles of Paragon and Renegade. Shepard can attempt
  to talk down Illusive Man in the same manner Saren can be talked down in
  ME1, resulting in Illusive Man committing suicide if successful.
  Anderson wants to destroy the Reapers while Illusive Man believes he can
  control them. Anderson will constantly fight the Illusive Man's
  indoctrinated logic and even say that he's been indoctrinated himself
  while Shepard seems oddly left out of the conversation except for key
  dialogues to sway the Illusive Man's opinion.
  
  The control panel
  itself is also a focus. It is located at the base of the Citadel Tower
  and is capable of opening up the arms of the Citadel when they are
  closed, however this seems to contradict events from Mass Effect 1. The
  control panel in the top of the Citadel Tower, in the Council Chamber,
  is known as the control panel for the entire Citadel.
  
  
  
  
  
  
  Sovereign had to link with
  the top of the tower to access the controls, after Saren reached the
  control panel in the Council Chamber to over-ride the modified Keepers.
  It is highly unusual that there is a secondary control panel in the
  opposite end of the Citadel Tower with the same functions as the main
  control panel, in a place that no organic has access to from anywhere in
  the Citadel (implied by Catalyst)
  
  
  
  
  
  
  The next portion of this
  scene is the elevator that lifts Shepard to the exterior area where the
  Crucible is connected, starting the meeting with Catalyst. The
  orientation of the hallway Shepard is dropped off in is unclear, since
  there is no view of the exterior of the Citadel anywhere to be seen. The
  assumption is that Shepard's head is pointing in the same direction the
  Citadel Tower is, yet the elevator at the Crucible console lifts
  Shepard up towards the bottom of the Citadel Tower, which either
  suggests that the elevator quickly switches around before reaching the
  exterior or that Shepard was, in fact, walking on the underside of the
  bridge connecting the Citadel Tower to the exterior ring that holds the
  arms.
  

  ---

  
  

  Arguments Against Indoctrination
  
  
  
  
  
  
  Please
  keep in mind that many of these arguments are not set in stone, and
  they exist in tandem with other arguments that counter them. However,
  because these arguments hold their ground in the realm of serious
  analysis (ie: pose a significant mental road-block to the theorist
  wanting to prove the null hypothesis), they are included here. Please
  see the post entitled "The Catalyst's Solutions" further down in this
  thread for the counterarguments against these queries.
  
  The
  explosion scene at the end of both the Destroy and Synthesis endings are
  a common topic of debate as to if Indoctrination is true or not.
  Shepard is on the Citadel when it explodes, standing in the EXACT
  epicenter of the explosion. Some say that Shepard fell from the Citadel
  and back to Earth, accounting for the rubble seen in the 'hidden' bonus
  scene. However, there are several flaws with this counter-argument.
  
  If
  Shepard was indeed on the Citadel when it exploded, there is no
  possible way the Commander would have survived the vacuum of space. The
  Commander's armor suit is severely damaged to the point where pieces of
  it are missing. The Commander would have died without that or the helmet
  on. Even if Shepard somehow survived, the trauma of re-entering Earth's
  atmosphere would have destroyed Shepard's body far worse than what
  happened after the Collector Ship attack in Mass Effect 2. Though the
  breathing scene ending is the only seen if Destroy with 5000 and above
  EMS is chosen, the likelihood of Shepard surviving the explosion, let
  alone re-entry into Earth's atmosphere is extremely unlikely.
  
  A
  further argument against Indoctrination is the Prothean VI discovered on
  Thessia. It has proven it is capable of detecting the effects of Reaper
  indoctrination, as it warns about Kai Leng shortly before he arrives in
  the temple. HOWEVER, this segment of the game can go both ways. The VI
  never says how much an individual must be indoctrinated to detect it.
  The Protheans trying to build the Crucible in their cycle were divided
  into two factions, a secondary sect that believed they could control the
  Reapers (sound familiar?). This secondary group turned out to be
  indoctrinated, yet the Prothean systems did not detect it until it was
  too late.
  
  Another argument against the Indoctrination Theory is
  the fact that arriving at the Catalyst with the lowest EMS rating
  presents the player with only a single option -- Destroy (if the
  Collector base was destroyed in ME2). Why would this option be the only
  one to exist, ever, if Destroy implies that Shepard breaks free from
  Indoctrination? Certainly, it implies his/her death, but does it also
  definitely imply the death of the Reapers? And if it does, why would it
  ever be presented to Shepard, regardless of the certainty of Shepard's
  impending death? Concurrently, if the player arrives at the Catalyst
  with the lowest EMS rating (and the Collector base was saved in ME2),
  the only option given to the player is Control. While this, at its most
  basic level, seems to support indoctrination, Shepard still dies with
  said EMS rating. What would be the point of Harbinger extending the
  option to Control to an organic about to die/be harvested?
  
  If the
  limited choices are presented because of a direct correlation between
  EMS rating, then why bother to have the meeting with the Catalyst at
  all? If Harbinger is aware that Shepard hasn't got enough military
  strength to help him sustain the indoctrination attempt, why bother
  bringing up to meet the Catalyst? The Reapers do not seem to be inclined
  towards any sort of emotional parlance -- one could argue that bringing
  an assuredly defeated (and soon to be annihilated) Shepard up to meet
  the Catalyst for an abysmal, empty, and sour single choice
  may be a
  bit... sociopathic. A final way to prove to Shepard that all his/her
  efforts have been in vain. But why bother? Such emotional manipulation,
  in this sense, does not fit the Reaper modus operandi. Reapers operate
  upon efficiency, at all times. Engaging in manipulation of an already
  obsolete hero does not beg efficiency.
  
  Another potential
  road-block to the indoctrination theory is the destruction of the mass
  relays that the Catalyst tells Shepard will occur, regardless of choice
  or outcome. If indoctrination was the ultimate goal of Harbinger, why
  would the mass relays be destroyed in a Control or Synthesis ending? How
  would this serve the Reapers?
  
  A final real-time argument against
  the IDT comes directly from BioWare itself. BioWare's wording about the
  endings suggest a lack of intention about IDT:
  
  "Building on
  their research, Exec Producer Casey Hudson and the team are hard at work
  on a number of game content initiatives that will help answer the
  questions, providing more clarity for those seeking further closure to
  their journey. You’ll hear more on this in April. We’re working hard to
  maintain the right balance between the artistic integrity of the
  original story while addressing the fan feedback we’ve received. This is
  in addition to our existing plan to continue providing new Mass Effect
  content and new full games, so rest assured that your journey in the
  Mass Effect universe can, and will, continue." -Dr. Ray Muzyka"
  
  This
  line of reasoning also poses an excellent challenge to the
  BioWare/Player Indoctrination sub-Theory. If BioWare's intention was to
  allow the player to experience indoctrination firsthand, why only
  present the possibility of one choice (thereby negating the potential to
  experience indoctrination)? After all, even though in reality, we can
  play the game multiple times to achieve the endings and outcomes that we
  desire, if Mass Effect was reality, Shepard would only have one chance.
  One chance, one choice, and no hope of respawning to try again
  (Cerberus implants excepted)...

Codex Entry on Indoctrination


Reaper
"indoctrination" is an insidious means of corrupting organic minds,
"reprogramming" the brain through physical and psychological
conditioning using electromagnetic fields, infrasonic and ultrasonic
noise, and other subliminal methods. The Reaper's resulting control over
the limbic system leaves the victim highly susceptible to its
suggestions.
Organics undergoing indoctrination may complain of
headaches and buzzing or ringing in their ears. As time passes, they
have feelings of "being watched" and hallucinations of "ghostly"
presences. Ultimately, the Reaper gains the ability to use the victim's
body to amplify its signals, manifesting as "alien" voices in the mind.

Indoctrination
can create perfect deep cover agents. A Reaper's "suggestions" can
manipulate victims into betraying friends, trusting enemies, or viewing
the Reaper itself with superstitious awe. Should a Reaper subvert a
well-placed political or military leader, the resulting chaos can bring
down nations.

Long-term physical effects of the manipulation are
unsustainable. Higher mental functioning decays, ultimately leaving the
victim a gibbering animal. Rapid indoctrination is possible, but causes
this decay in days or weeks. Slow, patient indoctrination allows the
thrall to last for months or years.

During the conversation
with Anderson and Illusive Man, Illusive Man will force Shepard, against
their will, to raise their pistol and shoot Anderson. Anderson will
take the shot in his lower left abdomen, but there is no blood spatter
or a bleeding wound and Anderson seems unaffected by the shot.

After
Illusive Man is killed and either Shepard sits down with Anderson or
alone in front of the console, Shepard will place a hand over their
lower left side, exactly the same spot where Anderson is shot. Shepard
is suddenly bleeding profusely from this wound

After waking up from
Harbinger's attack, the landscape behind and around Shepard seems
strangely devoid of debris (like downed gun-ships and several MAKOS).
The surrounding area is also strangely blurred beyond recognition and
buildings seem to be either missing or very far away, especially in the
direction Shepard just came from. There also seem to be less bodies than
there should be on the battlefield.


James Vega will comment on
hearing a humming sound down in the shuttle bay during a short
dialogue. The Normandy's engines run silent or at least very quietly (as
commented by Tali from ME1), so the humming's origins remain a mystery.
Video link provided by Murasame

The pistol Shepard
picks up after Harbinger's attack requires no thermal clips or
reloading, though you can reload the pistol. The pistol is suddenly gone
after going through the Citadel Beam. Shepard will pick up the pistol
again after taking a few steps down the hallway. The pistol disappears
again after Illusive Man dies, then Shepard will suddenly be armed with
it after the conversation with Catalyst.

When Shepard wakes up,
you will hear Coates speaking with a woman about Hammer Squad. According
to Coates, none of Hammer Squad made it to the Citadel Beam. Coates
must have a view of the area from somewhere yet does not see Shepard get
up and limp towards the beam. No survivors from Hammer Squad or anyone
who has view of the area seems to realize Shepard is up and moving.

Anderson
contacts Shepard after reaching the Citadel and claims to have come in
behind Shepard... yet, if you swing Shepard around to look behind them
while heading towards the beam, you will see no one behind you. Anderson
also mentions 'we' as if others with him made it to the beam as well.

During
the second and third nightmare, the 'oily shadows' will appear in
semblance of human figures, surrounding the Vancouver boy. Shepard will
also hear the voice of either Kaiden or Ashely and any other companions
that have died during ME3.

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Circumstantial Evidence

Harbinger
has no dialogue in the game and leaves the Citadel beam after Shepard
regains consciousness. Harbinger's voice actor from ME2, Keith
Szarabajka, is not credited specifically for Harbinger in the credits,
only for Additional Voices.

A heartbeat can be heard in the audio track when Shepard/Player makes their decision at the end of the game.
Audio extracted by Predalienguy - ME3: Heartbeat

On both the battlefield
and the hallway we see piles of corpses. The ones seen on the
battlefield are to Shepard's left (and right I believe) and lack any
distinction, just mostly textures of what appears to be the Phoenix
armor and a couple of others seen from Mass Effect 1. These bodies
reappear again in the hallway on the Citadel.

Some of the bodies are
more distinctive models, though we also see Alliance Marines added to
the pile. The features on the models are flat and generic and do not use
the face system in Mass Effect 3 like it does for all NPCs. This pile
of bodies also appeared in the Collector Ship when it was disabled.

The
route to the control panel appears similar to areas Shepard has already
been, like the Collector Ship, the Shadow Broker's Ship, and several
Cerberus bases and facilities.

Anderson makes it to the console
before Shepard despite the lack of any other connecting routes to the
room. Though he does mention the shifting walls, when Shepard sees them,
there is no connecting pathways hidden or revealed. Illusive Man also
comes in from behind Shepard from the same route Shepard took. There is
no where in the room to hide or enter from aside from the door Shepard
came through.

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Disproven/Debunked Evidence

The
trees seen after Shepard wakes up after Harbinger's attack don't seem
to bear much significance aside from simply populating the area. They
appear out of place among all the chaos, but their purpose seems to have
no deeper meaning