So, to the meat of the issue:
We have already established as much evidence as we can that 'proves' that Shepard is either hallucinating/dreaming just prior to/immediately after he runs into Harbinger's beam/Conduit. The hallucination/dream sequence has been quite well fleshed out, with a lot of compelling environmental evidence to support it (again, please see page 1 for further analysis). I am going to use this particular vehicle of suspension of disbelief to propose that BioWare's intention during this sequence is to flag the player with as many markers as they can: This current reality playing before your eyes (the Citadel, the Catalyst, TIM, Anderson) is a reflection of Shepard. It is the product of his/her mind. The meeting with the Catalyst may or may not be rooted in reality; they may meet in some metalphysical dimension, or Shepard may just hallucinate the entire thing. Either way, this theory would argue that it essentially doesn't matter, because what truly matters is the role of the player in this sequence. Your role. The scene is set in a way that urges the player to become aware of things just not being right, of being a place that mirrors (literally) Shepard's experiences throughout the game. The reality presented on the Citadel is an amalgamation of archetypes of every thing Shepard has seen in the series, which this theory challenges the player to understand as being adirect prompt from BioWare to understand that what is truly happening during this scene is all within Shepard's mind. His/her reality. Under her/his control.
Understanding that the reality on the Citadel as being a cerebral concoction that is entirely of Shepard's creation is important when we arrive upon the Crucible. It becomes a vital understanding when we are faced with these three, seemingly bizarre and unexpected choices that the Catalyst gives us. This theory submits that BioWare is asking the player to actively question EVERYTHING that happens once Shepard runs into Harbinger's beam. The cost of not questioning, or making the right choice even if you do?
Real-time player indoctrination. Shepard's literal death.
Think about it carefully. We arrive on the Crucible, and are faced with an archetype of manipulation, the Catalyst. Taking the form of a child that has come to represent everything that is horrendous about the Reapers to Shepard, the Catalyst/Harbinger provides Shepard with three strange and disorienting choices. He first presents Shepard with the option of Destroy, making swift and empty assertations about how it is the wrong choice because it would kill all synthetic life and Shepard herself/himself. At its surface, this seems like the renegade/chaos option, and is even insidiously portrayed in Renegade Red, a direct nod to the Player himself/herself. Directly appealing to your experiences with how the game works. He then goes on at great length about the Control and Synthesis options, portraying Control as the blue paragon/order option. Again, directly appealing to the Player. He arguesthat Control is the best option, implies that Shepard is the new Catalyst, and leaves us to contemplate the possibility that we could use it to try and save the people we love; after all, we are Shepard, and we would never become like TIM.
Synthesis is the last option explored, and it is portrayed as a compromise or as being the Brave New Hope for the galaxy. I have a suspicion that Synthesis may actually be the 'perfect' choice, but thatis for another theory.

(If you're curious, read about the tech-singularity lore within the game, and research humes spork's posts about the singularity within this thread.) Either way, Synthesis smacks of strangeness because it seems so inherently Reaper-oriented. As though it were servicing the Reapers' philosophy more strongly than the other two options.
This moment, when you are standing there, agonizing over your choice? This is your indoctrination moment. This is where, it could be (fantastically and insanely) argued that this is the moment when indoctrination and all of its insidious power becomes as real as it possibly CAN be to the Player. Think about it! We stand there. We agonize. We freak out about the ridiculous choices, and we wonder (like Shepard would) why we just can't ARUGE with the Catalyst (like Shepard would). And then, as this reality seems to be the only way forward (much like how indoctrination presents a version of reality to the indoctrinated that he/she sees as being the ONLY REAL OPTION -- echoes of TIM, Kai Leng, Saren here), we begin to accept it. Tremulously, we start to make our choice.
If you choose Control, then you, the player -- the one who moves through the game though Shepard's eyes; every choice s/he has ever made in the game has been directly because of you -- have been indoctrinated. It mayhave been because you thought you could save your crew, your LI, or that you really could gain perfect Control over the Reapers because you are Shepard. Regardless, you have been duped. Indoctrinated by the game.Your slow exposure to the Reapers in 2007 culminates to this final choice -- complete and free player agency and determination.
If you choose Synthesis, you face a fate similar to that of Control. It's debatable to me at this point as to whether or not you have chosen to fulfill the Reapers' purpose, but indoctrination is still a heavy possibility with this one. The only reason that I state this with any certainty is because, like the ending we see with Control, Shepard is dead at the final credits.
If you choose Destroy, then the Player Indoctrination Theory submits that this is you, the player, deciding whether or not Shepard overcomes the indoctrination attempt being rained upon him/her by Harbinger/the Catalyst. If you decide this option, and if you have enough EMS to ensure that Shepard has enough real-world time to get through the indoctrination attempt/hallucination -- Shepard lives. We see him/her breathing in the rubble of London streets at the end of the game. Shepard has defied indoctrination. You, yourself, have defied indoctrination.
Does this theory make sense? Maybe not. When we consider BioWare's real-world motivations and risks (profit, losing a large fanbase over the disgusting wretchedness of the endings as they currently exist), then the theory is hard to support. But if, for just one moment, we can let ourselves believe that BioWare may just have lived up to their celebrated philiosophy of Player Choice and Player Acutalization, then this theory becomes awe-inspiring. Is it possible? Could BioWare have sacrificed the potential for safe profits in order to bring the most insane and beautiful gaming experience of all time to its fans? The most unprecedented example of player immersion of our times? Would BioWare have truly allowed the risk for profit and angering a serious amount of their fan population in pure deference to the story, and its lore?
It may explain BioWare's silence on the matter, until "more people have played the game", or until all regions have the game. It may explain Jess M.'s twitter about fans "reacting before having all of the facts". It may.... just may explain these super sh*tty endings in a way that would make BioWare the God of RPGs.
Lastly from myself the originator of this note: Many people say that if your EMS is low you can only choose destroy, and you die anyway. Mass Effect has punished lazy shep since ME2. With you dying if your teammates aren't loyal or ship not upgraded. You can in ME2 defeat the collectors, and still die (but it isn't canon). So this might apply to ME3. You have a low EMS score, then you can beat indoctrination, but you will die leaving DLC/Continuing the story pointless just like in ME2.
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If this is true that would indeed be the Ballsiest move in gaming history.
But it would probably make them complete moneygrabbers, if they then later continue the story through dlc (which 9 outta 10 time you gotto pay for).
But it would be cool if they actually did this and then later put out free dlc that continues the story after you made that indoctrination choice.