So I just finished the trilogy about a week ago and I have been mulling the ending over in my head. I have also delved into the indoctrination theory. This is my take on everything I have pieced together (note I have not played the dlc just watch cutscenes as I discussed, I especially encourage feedback here to help fill in any blanks I may have):
Few things first. Dreams relate heavily to fighting indoctrination, from voices, shadows (oily shadows as the rachni queen mentioned?) the child no one acknowledges, and the burning at the end of each dreams. There are other clues threw out the game to suggest that Shepard is fighting indoctrination, but I will leave that in IT theory as there are quite a few (IT also has a lot of clues I think are to flimsy to give credence)
First I think some of indoctrination theory has solid ground, as well as outside evidence (such as tweets mentioned in the documentaries). Bioware has never confirmed this theory though, and dlc events have added what many see as conflicts to IT. I think that IT has the right grounds, but goes farther that it needs to. So lets start at the begging (note: I will not go over all evidence in IT, just things I feel were deliberate and premeditated in the games creation.)
First, Harbingers beam. I direct Reaper beam kills everyone, including Shepard as demonstrated in a previous fight with a reaper on Rannoch in mass effect 3. Though when you are hit by the reaper beam on Rannoch it simply glazes over you and you crumple. No white light! Here is the catch I noticed, Harbingers beam did not actually hit Shepard (or at least the did not show that) you can argue this one all you want, but empirically you cannot say the beam definitely hit Shepard simply because the screen whites out before it happens. He is likely just caught be the beams splash damage so to speak.
Second the first two scenes of the citadel. First you land in a dark room that appears to be a processing center for organics. You are awakened when you hear your name and there is a pulse that jars you awake. I don't think this has any exact purpose other than ambiance that something is off. Then you listen to Anderson as you make your way to the citadel, but Anderson's wondering almost seem to be guiding you rather than explaining anything. So all of that is a bit speculative, but I feel serves a vital roll in creating this strange ambiance for the confrontation ahead. So here there are a bunch of tidbits that suggest this scene is not completely physical, and I will try to be as concise as I can. First every time the illusive man speaks there are dark wavy shadows over the edges of the screen (possibly the inky shadow reference?). Second, after Shepard shoots Anderson in the abdomen, and the conflict resolves, Shepard is the one left with the wound. But what if you let Anderson die? Anderson represents the resistant of you in this theory and the illusive man represents the indoctrinated, but not you as a whole. More like the devil and angels on your shoulders trying to convince you of a process, in the end even with there council you are the one with the decision to make. Even if Anderson dies all you have lost is his council or advice, you still resist defeat indoctrination and kill the illusive man/devil on your shoulder. Take not the echos in here, and the fact that each side is always speaking and looking or facing you, even when they are fighting each other. I get a distinct feeling of an inner struggle threw out this scene it screams internal conflict and not physical confrontation. Then in the final scene of this room you wander over to the station and fall, next a pad lifts you into the air and to the outside of the ship. Then when you arrive (out in space, you can see exactly where you are and earlier pictures of the catalyst docking with the citadel depicts that location is on the exterior of the citadel!), but you are no longer facing the correct direction. This change seems to be intentional since the extended version didn't change it.
Third the scene in the decision chamber of the citadel. Your position is changed and you are not asleep, but you do not move as if frozen until the starchild (for simplicity I will refer to it as the starchild not as the catalyst or the intelligence) says "wake up" the you merely move to a injured but standing position. Here the starchild explains itself, the reapers, and the cycles existence and purpose. Once again echos, a phantom child (the one that you see from the beginning but no one acknowledges), and he has the voice that is both Shepard and his own (both male and female Shepard voices were used.) To me there are still alot of dream or vision like influences/ambiance in this scene, but the starchild is obviously giving you free will here, not imposing will or reason on you. Unlike the indoctrination theory I think that this is directly a communication with the starchild. Also, it does not have a reaper agenda, the reapers have its agenda! since it made them for there purpose. So of course it reasons that destroy is the worst option, that would simply be throwing away all its work. But the starchild acknowledges his flaw in design and is asking for shepards help. Note that this chamber is similar in design to the ground of earth by the beam. It seems reasonable that left and right options actually are represented by the spires next to the beam. Notice that each choice is activated not only in a different location, but in a different manner. Perhaps the location is irrelevant, because it is how you interact with the object that counts, and the vision is simply distinguishing between which action you are willing to go. Perhaps you are still on earth and how you interact with the beam there discharges the citadel in its given way. Next lets look at the actual decision. After getting attacked by Harbinger and before you conclude your final choice, you are injured. Once you make your choice and your resolve hardens you are given new vigor (this is distinct because at the start of the final choice cut scene you are still injured just for a second then you straighten up and commit your decision with complete resolve, it isn't just an oversight when making the cut scene it is distinct.) This tells me that it is your will power tell is determining your stature not your physical state (even after you defeat indoctrination you are lost and don't know what to do before the starchild explains.) The Leviathan dlc discusses "the intelligence" and makes it obvious that he is the "catalyst". So we know the starchild is more than just Harbinger trying to trick us, but the physical form of starchild is never discussed meaning for all we know this entity is simply digital existence that can travel between reapers and or the citadel without actually have to contain a body. It also stands to reason that if the reapers can indoctrinate people, the starchild could also influence our minds, and with as advanced as it is described perhaps enter our minds all together. We are mysteriously brought to the starchild after defeating the illusive man/indoctrination. Shepard would be the only known person to accomplish this. Perhaps this is the reason the starchild gives him/her the power of the reapers and the galaxy for Shepard is the only one worthy of decided its fate. Notice the fourth ending? I believe this is to re-enforce that the starchild is giving Shepard complete faith in deciding the best course of action, even it it goes against exactly what the starchild just said it didn't want to do.
Finally the chosen ending. First I think that the extended cut demands the ending "slideshow" as a physical ending not a dream/vision. Also notice no echos, shadows, or other dream like ambiance. The previous ten minutes felt very wrong to me at first and I couldn't place it. Sure I could name things I felt were wrong, but not the over arching problem from the time I entered the citadel. Until I considered that I was not actually on the citadel and the events were not real/physical. That seemed to fit the best, but when the citadel goes off it is like a lens suddenly coming into focus. Everything comes off sharper and more energetic than before. The ending speeches have real purpose in the physical universe and there is no ambient changes when shepard takes his breadth (if you chose this path.) this leads me to believe that from the time the citadel goes off you are back in reality, witnessing your actions in your vision physically manifest (possibly from interacting with the beam you were near on earth.)
I am sure there are plenty of things I saw that I left out, it is late now, but I couldn't hold this any longer I had to put it up for discussion (if anyone is interested.) I think that this theory resolves everything that bothers me about the "take it as it is" and the "indoctrination theory" approaches, because neither one sites perfectly with me. What do you think does this theory stand up? where are the biggest flaws or is it reasonable given all the evidence? do you think that this is more plausible that either the take it as it is or indoctrination theory, given the extended ending and dlc evidence?
Note: still find it strange that if you choose synthesis or control your eyes have the same eyes as the illusive man (I don't see the same pattern in sarens can anyone share a link to an image that denotes that?) does this insinuate indoctrination?
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I love how everyone forgets about the squadmates.
