From my blog, http://frillin.radbox.org/ , which is general audience, so have patience with the exposition that might not be needed for the Gamespot crowd...
WARNING: This piece contains massive spoilers for the Mass Effect trilogy. If that's going to be an issue then you need to get out of here right now!
There's been a lot of hoo-haw about the final moments of the Mass Effect trilogy. In response to what a lot of people have deemed an "underwhelming" or **** ending, a rather interesting theory has popped up. It's called the Indoctrination Theory, and it states that the events in the final moments of Mass Effect 3 are not to be taken literally, but rather all occur in the protagonist's (Commander Shepard's) mind as he (or she, if you chose a female Shepard) fights against Reaper Indoctrination, an insidious form of mind control employed by the genocidal synthetic Reapers who are in the process of killing all advanced organic life in the galaxy. While it's an interesting and remarkably plausible theory, I think it would be a crime against everything that Mass Effect is for Bioware (the game's developers) to establish Indoctrination Theory as the canonical reality.
I'm going to indulge myself for a few paragraphs and talk about my non-ending related Mass Effect experiences. Feel free to skip ahead, you won't miss the thesis.
*** Begin indulgence***
For a story that spans an entire galaxy, the beating heart of Mass Effect is actually something much, much, smaller. It's not the story of myriad species eventually coming together to battle a common foe; it's the story of a wise and gifted Commander Shepard, who has been charged with a series of impossible tasks, and a close circle of friends and allies who have sacrificed everything to give him a chance to succeed. It's about a would-be hero who went against all odds trying to save the galaxy, only to watch the best and brightest souls in that galaxy be ripped away before his eyes.
By the time I reached the final moments of Mass Effect 3, I didn't feel like there could be such a thing as victory. I had tried to remain stoic in the face of the insurmountable odds, but (and it pains it me say this, given how much of a dick he had been to me in the past) Kaiden was right: this is the end. And while there was still plenty of light in the galaxy worth saving, like the newly freed geth, the homeward bound Quarians, and the genophage-free Krogan, I couldn't help but feel that the brightest lights in the galaxy had already been extinguished. I thought of Mordin, sacrificing himself at the Shroud because he couldn't trust anyone else to get the job done properly, or Thane, whose dying action was to pray for my soul. I thought of Kelly, who had been saved from the collectors only to be shot in the face by a vengeful Cerberus. If anything had been worth saving, it was them, and now they were gone.
There were still good moments to have. Having a good laugh with Garrus as I beat him in a shooting contest atop the presidium, making some sort of peace with Kaiden, and seeing Jack put her talents to good use all helped ease the burden a little bit. They were still alive and kicking, and that felt like more of a success than any victory over the Reapers ever could. They had all somehow found their peace as the result of this crazy journey. However, I could tell that they, like the rest of the galaxy, needed Shepard, if not to save the universe than to have someone they could believe in, someone they could always count on to help them out when they had run out of hope.
*** End Indulgence***
So after a long and treacherous fight through Reaper-controlled territory (on the "Insanity" difficulty, no less) there it is, the now infamous choice to be made about the Reapers: control them, destroy them along with all other synthetic life in the galaxy, or fuse with them in "synthesis". I found the decision to be agonizing for any number of reasons. Synthesis promised to be the final step, ensuring that the cycle of Reaper violence would end for good and that some other poor commander would not have to watch their friends die one by one in 50,000 years the way I had. Destruction promised a clear-cut solution to the Reaper problem. There was the threat that the surviving organic species would re-create synthetic life, putting us back where we started, but I figured that it was their choice to make, and that if they blew their second chance by recreating the Reaper problem that it would be on them. Control promised... well, it's hard to say. It could bring a peaceful end to the Reapers' genocide, but it was hard to shake the ghost of The illusive Man, the antagonist whose efforts to control the Reapers left him a hollow shell, enslaved by the very power he sought to harness, and whom I had spent the entirety of Mass Effect 3 defying so that I would have the opportunity to destroy the Reapers.
I made my choice, and I don't think that the choice itself matters so much as why the choice was made. I chose to control the Reapers, not because I desired an army of killer robots to do my bidding, but because I wanted some way to get word to my friends and loved ones that everything is all right and that I'm proud of them. I took control of the Reapers because while we had all said our goodbyes before the final suicide mission, it was under the shadow of our pending annihilation. I wanted a chance to say goodbye under better circumstances, and of the three choices, only this one gave me that opportunity. It's as bittersweet as endings come, and I thought that it was an absolutely beautiful finish to an incredible and personal story.
That is, of course, unless the Indoctrination Theory holds true. It states that all I did was submit to the Reaper Indoctrination, that choosing to control the Reapers was simply me being unwilling or unable to make the admittedly far more difficult choice to "destroy" the Reapers (and a lot innocents along with them), which would actually represent Shepard breaking free of the Indoctrination. This is pretty cool, I must admit, but it would ruin everything for one very simple reason: moral luck.
The "regular" (non-Indoctrination Theory) ending to Mass Effect is, to me, brilliant. Each choice has equal doses of bitter and sweet, and the stakes and consequences are clearly laid out. Your choice reflects what you value in the Mass Effect story. If you see it as a story of organics vs. machines fought to the bloody end, you choose to destroy the Reapers. If you see it as the story of a new day dawning, you choose synthesis (which actually smelled a bit like Battlestar Galactica to me). I saw it as the story of a Commander and the people that made the galaxy worth saving, and that led me to choose control. Your choices matter because you know what you're getting into, and you can walk away knowing that this imaginary world that lives inside your computer is a reflection of what really matters to you.
The Indoctrination Theory ruins all of that because it changes your choices into a coin flip. It essentially says "hey, do you think that you are indoctrinated and that by choosing to destroy the Reapers that you can break free of it?" The choice you make now has nothing to do with what you value and everything to do with whether or not you think Bioware is **** with you. It's called "moral luck:" you might make the "right" decision of "destroying the Reapers" (since the other two are just you lying down and taking it from them) but there are so many unknowns that it's pretty much a shot in the dark. Sure, it all works logically, and I'm not saying that I have a problem with an ending as grim as "you were too weak to free your mind, and now we're all Reaper food, so thanks for that." I think a dark ending like that is just fine, but in an experience such as Mass Effect, which has given players a collaborative part in storytelling unlike anything we've ever seen before (and reminds us of why interactive stories can be so much more compelling than anything in a book, TV show, or movie), it seems diminishing and ultimately unnecessary to take the most significant choice in the story and not just remove it, but possibly invert it.
So if you're Bioware (which has announced that extended endings are en route) what's the solution? I think it's rather simple: don't do anything. Mass Effect has always been whatever the player has wanted it to be. There's enough there right now for the Indoctrination theorists to accept their theory and feel clever about their find, and there are enough holes in it for the purists to reject it. Let Mass Effect die the way it lived: however we, the people who lived through it and were overjoyed to call the Normandy our home away from home, choose to remember it.