I'm going to stump for the indoctrination theory again.

Reasoning:

1) After reviewing the Shepard dream sequences again, the dead figures show up as inky blots (which is how the Rachni queen referred to indoctrination in ME).

2) There are some references to buzzing or humming sounds when Shepard is around

3) The final sequence: Just way too many questions/inexplicable things for this to be just poor game design.

- Why does Shepard have a gun with unlimited ammo? Seriously, you can sit there and just pound away with that thing for however many shots in a row you want. Complete violation of the game mechanic. Mistake?
- How does Anderson get to the station before Shepard? How does he beat Shepard down the only hallway to the control console?
- How is the Illusive man able to control Shepard and get him to shoot Anderson?
- Why does you see inky blackness at the edge of the screens when the Illusive man is trying to influence Shepard (as he holds his head)
- Why does Anderson look at Shepard while saying things such as "You're indoctrinated!" to the Illusive man?
- Why does Shepard only notice he's bleeding from a wound in his left side ONLY after Anderson "dies" (coincidentally, the same wound Anderson took from Shepard's gun)
- Why is the final sequence so inexplicable. The Normandy is suddenly in space AND in the middle of a Mass Relay jump. Your squadmates from the last mission somehow: 1) Survived the charge to the beam with no wounds and 2) were transported to the Normandy before its jump
- The only other time we've seen the destruction of a Mass Relay, it caused the system's sun to go nova. How does Earth survive this fate?
- Doesn't the synthesis thing sound an AWFUL lot like Saren's plan? Wasn't Saren ALSO completely unaware he had been Indoctrinated?
- Why is the ONLY way to get the "best" ending to do the "red" or "renegade" or "bad" option?

Lots of reasonable stuff with some video evidence backs it up (some good stuff on YouTube if you take the time).

And it makes the ending - and the entire third game and really everything done since the mission on Arotoht, a great, big mind-f***. That's the type of thing Bioware LIVES to do.

The final mission on the "Citadel" wasn't Shepard fighting to win the war against the reapers. It was Shepard fighting to win the war for his mind. He defeated the indoctrination. The reapers and relays haven't been destroyed, but his mind is his own. Winning by "synthesizing" or "taking control" are false victories seen only in his mind - and that's why Shepard can't survive. Winning by "destroying" the reapers gives him his mind back.

And they still have the chance to address this/expand on it in DLC or even a future game.

If the entire story arc was set up to cleverly conceal that Shepard was indoctrinated, they wouldn't just blow that in a press release.

I have nothing to do with the ending beyond a) having argued successfully a long time ago that we needed a chance to say goodbye to our squad, b) having argued successfully that Cortez shouldn’t automatically die in that shuttle crash, and c) having written Tali’s goodbye bit, as well as a couple of the holo-goodbyes for people I wrote (Mordin, Kasumi, Jack, etc).

No other writer did, either, except for our lead. This was entirely the work of our lead and Casey himself, sitting in a room and going through draft after draft.

And honestly, it kind of shows.

Every other mission in the game had to be held up to the rest of the writing team, and the writing team then picked it apart and made suggestions and pointed out the parts that made no sense. This mission? Casey and our lead deciding that they didn’t need to be peer-reviewe.d

And again, it shows.

If you’d asked me the themes of Mass Effect 3, I’d break them down as:

Galactic Alliances

Friends

Organics versus Synthetics

In my personal opinion, the first two got a perfunctory nod. We did get a goodbye to our friends, but it was in a scene that was divorced from the gameplay — a deliberate “nothing happens here” area with one turret thrown in for no reason I really understand, except possibly to obfuscate the “nothing happens here”-ness. The best missions in our game are the ones in which the gameplay and the narrative reinforce each other. The end of the Genophage campaign exemplifies that for me — every line of dialog is showing you both sides of the krogan, be they horrible brutes or proud warriors; the art shows both their bombed-out wasteland and the beautiful world they once had and could have again; the combat shows the terror of the Reapers as well as a blatant reminder of the rachni, which threatened the galaxy and had to be stopped by the krogan last time. Every line of code in that mission is on target with the overall message.

The endgame doesn’t have that. I wanted to see banshees attacking you, and then have asari gunships zoom in and blow them away. I wanted to see a wave of rachni ravagers come around a corner only to be met by a wall of krogan roaring a battle cry. Here’s the horror the Reapers inflicted upon each race, and here’s the army that you, Commander Shepard, made out of every race in the galaxy to fight them.

I personally thought that the Illusive Man conversation was about twice as long as it needed to be — something that I’ve been told in my peer reviews of my missions and made edits on, but again, this is a conversation no writer but the lead ever saw until it was already recorded. I did love Anderson’s goodbye.

For me, Anderson’s goodbye is where it ended. The stuff with the Catalyst just… You have to understand. Casey is really smart and really analytical. And the problem is that when he’s not checked, he will assume that other people are like him, and will really appreciate an almost completely unemotional intellectual ending. I didn’t hate it, but I didn’t love it.

And then, just to be a dick… what was SUPPOSED to happen was that, say you picked “Destroy the Reapers”. When you did that, the system was SUPPOSED to look at your score, and then you’d show a cutscene of Earth that was either:

a) Very high score: Earth obviously damaged, but woo victory

b) Medium score: Earth takes a bunch of damage from the Crucible activation. Like dropping a bomb on an already war-ravaged city. Uh, well, maybe not LIKE that as much as, uh, THAT.

c) Low score: Earth is a cinderblock, all life on it completely wiped out

I have NO IDEA why these different cutscenes aren’t in there. As far as I know, they were never cut. Maybe they were cut for budget reasons at the last minute. I don’t know. But holy crap, yeah, I can see how incredibly disappointing it’d be to hear of all the different ending possibilities and have it break down to “which color is stuff glowing?” Or maybe they ARE in, but they’re too subtle to really see obvious differences, and again, that’s… yeah.

Okay, that’s a lot to have written for something that’s gonna go away in an hour.

I still teared up at the ending myself, but really, I was tearing up for the quick flashbacks to old friends and the death of Anderson. I wasn’t tearing up over making a choice that, as it turned out, didn’t have enough cutscene differentiation on it.

And to be clear, I don’t even really wish Shepard had gotten a ride-off-into-sunset ending. I was honestly okay with Shepard sacrificing himself. I just expected it to be for something with more obvious differentiation, and a stronger tie to the core themes — all three of them.