Why do you not believe the indoctrination theory? *Major Spoilers*

[SS2Dante]

I'm kind of in the middle ground here. I think everything that happens post-Harbinger beam does actually happen, but I also think that Sheppard is indoctrinated by that time. The idea that the whole thing is a hallucination is just way to elaborate for me. That's the one part that DOES seem like a desperate attempt to retcon the "Star Child". I think that all the plot holes/twists are just the result of lazy writing, but if Shepard is indoctrinated, then at least his sudden and complete reversal of moral reasoning makes some kind of sense.

You know, that bit with Joker would be really easy to explain, too. They just need one line from Hackett telling the fleets to get everyone they can and run for it if they see the Crucible preparing to fire. It would make sense: Once it goes off, it's either to destroy the Reapers or it isn't. Either way, there's no point in waiting around to find out, especially considering that whatever it does will most likely involve destruction on a massive scale. One quick cutscene of Joker picking up your squad (along with showing a few casualties based on the player's performance)as the Crucible prepares to fire and we're good to go.

Hackett giving an order that, if the Crucible is about to fire, every ship is to collect it's passengers from the war torn earth and run? Leaving the Crucible defenceless? Either it fires with barely any warm up (no time to run) or it fires with a long warm up (Reapers can destroy it).

Ok, how about this - here's the 3 options you get from the child.

Control (blue/paragon) - take control of the Reapers. Think we can all agree this is how the Illusive man was indoctrinated?

Synthesis (neutral) - combine all life into a new version of life, both synthetic and organic. The pinnacle of evolution. THIS DESCRIBES A REAPER. Notice in the end video nothing appears to have changed with regards to life.

Destroy/Fight (red/renegade) - this choice is presented as the evil one, since it entails killing millions of innocents. It's also the only one that doesn't result in Shepard dissolving into nothing. This ending gives an extra cutscene of Shepard waking up in rubble.

The evil choice is the only one that doesn't involve giving up and dissolving into nothing. It is also the only one with the extra cutscene. If you don't believe the indoctrination theory how do you explain it?

 

[SajuukKhar]

I'm going to ask a question here and I do so as someone who has only played the original Mass Effect but knows a fair amount about ME2 from spoilers and some of ME3, but particularly having seen the endings in their entirety and reading quite a few of the theories and discussions on them. Why, if Harbinger is right there and can easily just kill Shepard (and seemingly tries to by blasting him) would he bother trying to indoctrinate him? To what end? To stop him from destroying the Reapers? Because killing him seems easier when he's right there and you just need to shoot him.

For probably the same reason the Anti-spirals from Gurren Lagann didn't just kill the gang when they had the chance.

They want to inflict absolute terror and despair.

Having Shepard, who is wildly seen as the hero of the galaxy at this point, indoctrinated would be a powerful symbol. It would show everyone that even their best failed to stop them.

 

[SS2Dante]

So in your theory the remnant's of the Normandy create a new race? That seems just as unlikely to me.

We've seen that knowledge survives the cycle. Even some species can (ala the Prothean). We don't even know that these two beings are human, or how many thousands of years have passed since the ending. The two beings could be a different race, hence the title of Stargazer instead of any actual name.

Only possible with the human/asari crew could, obviously. It isn't "my theory" so much as the conclusion most people have seemed to have reached about it. Sans indoctrination. My theory is that the endings are just bad.

At any rate, if what you say is true then we've lost in all the endings barring a retcon. And you have to read another cycle of extinction and a new humanoid race into it. See what I mean? To reconcile that tiny scene, you have to make up a hell of a lot. If the endings are literal and just bad, it is there to establish your ultimate victory and sell dlc. The indoctrination theory is supposed to interpret what is there to the reconcile the plot holes. It fails to account for the final-final scene of the game without creating new plot holes. It isn't discussed in the article because it blows the whole thing out of the water without a ton of spackle.

What plot holes? In follows logically that if, in two of the 3 endings, we lose to the Reapers, new life evolves afterwards. This has been established.

In the red ending, we haven't seen what happens next. We got a cliffhanger ending. Therefore we may have survived, or died. Neither of which contradicts my point.

Also, about that scene with Joker and the Normandy - they're going at Mass Effect speed when it hits them. Either they die right there or, if they somehow got to the end of the jump in time, they'd be killed by the explosion.

 

[SS2Dante]

Can someone confirm the part about turning around and seeing the trees after Harbinger's blast? I'm letting a friend borrow my copy so I can't check for myself.

That part seems the most interesting to me.

Also, are we still giving Princess Zeelda the time of day? C'mon, guys. We're better than this.

I checked. There are a few trees alread there to the right of the beam, but when you wake up there's one directly behind you. I couldn't see it when I tried, but something maaay have been in the way. Jury's out.

 

[XMark]

You can take just about ANY story, work from the premise that the main character is mind-controlled or crazy, and make ANY ending you want from it, which is why the indoctrination theory is weak. Here's an example:

Jesus was actually a con artist who eventually ended up believing his own BS. Then one day when he saw people selling stuff in the temple he flipped out and killed some people. He was actually on trial for multiple murders but he imagined it was something else.

 

[SS2Dante]

I said it in another topic but an indoctrination ending would only be good if you suddenly lost control of Shepard and watched him make the choice for you like what happenned in Bioshock when you meet your dad face to face. It would be sad ending, and frankly horrifying to watch as we see the fallen hero damning the galaxy to another cycle, but it would be a better ending than the current set.

The beauty of this ending is that it wasn't Shepard who was indoctrinated - it was the player. WE picked the endings, which, when you look at them, are all (barring fight, the one noone picked cos it sounded evil) methods of indoctrination. Control the Reapers? That's how the illusive man fell. Create a new being, both synthetic and organic? That's what the Reapers are already doing.

 

[Ilikemilkshake]

Snip

Here's a quote of Boag linking me to a topic which contains the link to the proof that Indoctrination was intended but cut from the ending:

Bioware just stated that the sequence where shep was indoctrinated was left out.

this Pretty much proves it was indoctrination

heres the thread

http://www.escapistmagazine.com/forums/read/9.354425-Bioware-allows-the-release-of-The-Final-Hours-of-Mass-Effect-3-a-tell-all-app-for-2-99-WTF#14074722

As for Star Gazer, it could be a race in the next Cycle, but still: Shepard fails if he/she picks 2 out of the 3 possible endings. Why would Star Gazer be touting the heroic failure of an ancient being who tried but ultimately never stood a chance against the Reapers? Yeah, it's a fun story to hear about how Shepard stopped Saren and the Collectors, but ultimately those are non-points considering that he/she essentially only won 2 battles but got his/her ass kicked when the real war finally arrived. Not really a legend of a grand savior that people would pass down. Beyond that: I'm pretty certain that the Star Gazer mentions something about peace being achieved thanks to Shepard no matter which ending you pick. I could be wrong on this though, don't remember every line from that scene, but yeah, Star Gazer is the big fat elephant in the room to the Indoctrination theory.

There's one thing you're forgetting. At one point Liara comes to your room and says she's been working on something to leave behind incase you fail and she asks you how you want to be remembered... It could be that the next cycle has discovered this information cache and perhaps even beat the reapers themselves.

For me, the game ends after Anderson and Shepard have a chat, Hackett asks whats going on and Shepard collapse for final and last time.
The game ends with total absolute failure of the organic races to defeat the Reapers. Shepard fought a long hard road, but end the end - failed to fire the weapon.
You don't need closure because you then know that everybody else will have died in that battle and the rest of the galaxy for the next 200 years will slowly be wiped out.

This is how i was actually expecting the game to end. I had my own theory before doing the final mission, that the crucible was actually a Reaper invention which they used to trick organics into concentrating all their resources into one doomed escapade, making them that much easier to beat in one fell swoop.

I'll wait to see if any DLC is released before i make either that or the indoctrination theory my canon ending.

 

[Shockolate]

Because not as emotionally invested as others. Played game. Loved every second of it. Not against the theory.

*sharp inhale*

Just don't care.

 

[Jodah]

To me it just seems like desperation. I would love if it is true and part of me hopes it is. But the realistic part of me doesn't think Bioware/EA is smart enough to do something like this. I've been surprised before but to quote Einstein: ?Two things are infinite: the universe and human stupidity; and I'm not sure about the universe.?

 

[Vivi22]

For probably the same reason the Anti-spirals from Gurren Lagann didn't just kill the gang when they had the chance.

They want to inflict absolute terror and despair.

Having Shepard, who is wildly seen as the hero of the galaxy at this point, indoctrinated would be a powerful symbol. It would show everyone that even their best failed to stop them.

But again, why does that even matter? The Reapers are supposed to be machines so why waste the effort to indoctrinate him if there's a chance he may beat it and destroy you all when you can simply kill him and no one can stop you after that?

I'd agree that indoctrinating him could be a powerful psychological weapon, but if victory is otherwise assured and you have nothing to fear except this one man being able to stop you then it makes no sense not to kill him. Particularly for machines who you'd expect to be far more rational and practical than any of the organic races. They shouldn't care if it takes the next thousand years to purge the galaxy really, so long as it's done eventually. So unless the races of the galaxy stand a chance without the crucible then there's no need to indoctrinate Shepard. If anything it would be counter-productive. And killing him and stopping them from completing their seemingly last ditch plan to try and stop the Reapers while wiping out a combined fleet in the process should be a pretty major psychological blow all on its own frankly.

I mean, maybe I'm missing something here since I haven't played the game and have only read plenty of spoilers, which is part of why I'm asking for the clarification.

 

[SS2Dante]

You can take just about ANY story, work from the premise that the main character is mind-controlled or crazy, and make ANY ending you want from it, which is why the indoctrination theory is weak. Here's an example:

Jesus was actually a con artist who eventually ended up believing his own BS. Then one day when he saw people selling stuff in the temple he flipped out and killed some people. He was actually on trial for multiple murders but he imagined it was something else.

Once again - please read the article and look at the evidence. It makes MORE sense than the ending's as most people understand them. That shouldn't happen. Not EQUAL sense, MORE sense. It explains things clearly and methodically. Even if it wasn't Biowares intention (doubtful) ithe indoctrination theory is rendered true by this fact.

Again - can someone PLEASE explain the extra cutscene with the red ending? Without the indoctrination theory it shouldn't be there. With it, it HAS to be there. Lo and behold. I can't see any other explanation that makes even a lick of sense.

 

[Da Orky Man]

snip

Yes, it explains a lot of things, but it opens up huge plot holes. For example, if you get a really low War Asset score, you ONLY get presented with the 'Destroy' option. So, why would the Reapers only give you the option to destroy them, and no others? It makes less than zero sense. Also, you only get the 'Synthesis' ending if you get over 3000 War Asset score, indicating that it's supposed to be the rarer choice. Again, makes little sense.
Another point is the Stargazer scene at the end. You get it no matter which decision you make, so it stands to reason that all choices prevent the Reapers from killing everybody. This again conflicts with the Indoctrination theory, since two of the options should lead to defeat.

Now for the second part.
The literal interpretation of the ending makes little sense, and is therefore not a good ending. The Indoctrination interpretation does fill in a few holes, but it makes others and also makes little sense.
So far, Bioware have had little to say on the matter. I currently hold ME3 as one of the best narratives I've ever seen, read or played. I'm not nearly as bitter as many. But they still messed up the ending. We wanted closure, rather than space magic and wild theories.
Appreciated if you could actually respond to this, as well as edit the OP to include the ploholes I mentioned.

 

[SS2Dante]

For probably the same reason the Anti-spirals from Gurren Lagann didn't just kill the gang when they had the chance.

They want to inflict absolute terror and despair.

Having Shepard, who is wildly seen as the hero of the galaxy at this point, indoctrinated would be a powerful symbol. It would show everyone that even their best failed to stop them.

But again, why does that even matter? The Reapers are supposed to be machines so why waste the effort to indoctrinate him if there's a chance he may beat it and destroy you all when you can simply kill him and no one can stop you after that?

I'd agree that indoctrinating him could be a powerful psychological weapon, but if victory is otherwise assured and you have nothing to fear except this one man being able to stop you then it makes no sense not to kill him. Particularly for machines who you'd expect to be far more rational and practical than any of the organic races. They shouldn't care if it takes the next thousand years to purge the galaxy really, so long as it's done eventually. So unless the races of the galaxy stand a chance without the crucible then there's no need to indoctrinate Shepard. If anything it would be counter-productive. And killing him and stopping them from completing their seemingly last ditch plan to try and stop the Reapers while wiping out a combined fleet in the process should be a pretty major psychological blow all on its own frankly.

I mean, maybe I'm missing something here since I haven't played the game and have only read plenty of spoilers, which is part of why I'm asking for the clarification.

Actually, if you have a weak enough army at the end of the game you don't get the indoctrination choices at all. This implies that the Reapers don't fear you and aren't actively working on indoctrinating you.

Also - Harbinger is personally interested in Shepard (ME2). If you've continued being awesome by getting a good army it makes sense he'd want you indoctrinated, not dead.

 

[SS2Dante]

snip

Yes, it explains a lot of things, but it opens up huge plot holes. For example, if you get a really low War Asset score, you ONLY get presented with the 'Destroy' option. So, why would the Reapers only give you the option to destroy them, and no others? It makes less than zero sense. Also, you only get the 'Synthesis' ending if you get over 3000 War Asset score, indicating that it's supposed to be the rarer choice. Again, makes little sense.
Another point is the Stargazer scene at the end. You get it no matter which decision you make, so it stands to reason that all choices prevent the Reapers from killing everybody. This again conflicts with the Indoctrination theory, since two of the options should lead to defeat.

Now for the second part.
The literal interpretation of the ending makes little sense, and is therefore not a good ending. The Indoctrination interpretation does fill in a few holes, but it makes others and also makes little sense.
So far, Bioware have had little to say on the matter. I currently hold ME3 as one of the best narratives I've ever seen, read or played. I'm not nearly as bitter as many. But they still messed up the ending. We wanted closure, rather than space magic and wild theories.
Appreciated if you could actually respond to this, as well as edit the OP to include the ploholes I mentioned.

Lol, this came up in the post above.

If you've got a really low war asset score the Reapers don't need you indoctrinated. They don't fear or respect you, and are not actively trying to indoctrinate you. Hence the fact that it's easier to break the thrall.

Again, there is absolutely no evidence that the Stargazer scene involves humans. Information and even species can survive the cycle, and as another poster pointed out Liara is storing your story on a device, in case you fail. It could be during the next cycle. Even in one there were rumours of the Reapers which survived from the Prothean cycle.

Since this causes no problems I can't see them as plotholes.

Edit - the fact that it was such a good narrative is what made me suspicious. These errors are not small, or minor, or anything. They're huge problems. People really believe Bioware, famous for this story and the detail in it, would suddenly make a million huge mistakes, RIGHT after getting hit by Harbingers beam? Don't buy it. A mediocre ending I'd understand, but not a broken one.

 

[RJ 17]

Snip

Here's a quote of Boag linking me to a topic which contains the link to the proof that Indoctrination was intended but cut from the ending:

Bioware just stated that the sequence where shep was indoctrinated was left out.

this Pretty much proves it was indoctrination

heres the thread

http://www.escapistmagazine.com/forums/read/9.354425-Bioware-allows-the-release-of-The-Final-Hours-of-Mass-Effect-3-a-tell-all-app-for-2-99-WTF#14074722

As for Star Gazer, it could be a race in the next Cycle, but still: Shepard fails if he/she picks 2 out of the 3 possible endings. Why would Star Gazer be touting the heroic failure of an ancient being who tried but ultimately never stood a chance against the Reapers? Yeah, it's a fun story to hear about how Shepard stopped Saren and the Collectors, but ultimately those are non-points considering that he/she essentially only won 2 battles but got his/her ass kicked when the real war finally arrived. Not really a legend of a grand savior that people would pass down. Beyond that: I'm pretty certain that the Star Gazer mentions something about peace being achieved thanks to Shepard no matter which ending you pick. I could be wrong on this though, don't remember every line from that scene, but yeah, Star Gazer is the big fat elephant in the room to the Indoctrination theory.

There's one thing you're forgetting. At one point Liara comes to your room and says she's been working on something to leave behind incase you fail and she asks you how you want to be remembered... It could be that the next cycle has discovered this information cache and perhaps even beat the reapers themselves.

"Could be", indeed. Then again, it could be two human descendants talking about how Shepard saved their species. We've once again fallen into the realm of speculation. There's no way to prove that Star Gazer is a surviving human or a surviving member of the next cycle, though the evidence seems to lean towards the former.

The fact of the matter is that the ending is just a huge mess due to what Hudson butchered out of it. There's no way to prove it one way or another and apparently that was the original intention, but there was much more evidence to support the Indoctrination theory which sticks with the theme of the rest of the game (James mentioning a strange humming sound, and of course if you didn't know Shepard was at least partially Indoctrinated after that first dream-sequence then you're just not paying attention to what's been said about Indoctrination in the previous two games, particularly ME 2). However as I mentioned in the topic of mine that I linked a couple posts back, the butchered up ending ruined any chance we had for getting answers, or at least a stable theory with no holes in it. I fully agree that the Indoctrination theory is very sound, ALMOST everything fits, but Star Gazer is a big middle-finger waved in the face of the theory. He's the loose end that just doesn't fit.

 

[SS2Dante]

Snip

Here's a quote of Boag linking me to a topic which contains the link to the proof that Indoctrination was intended but cut from the ending:

Bioware just stated that the sequence where shep was indoctrinated was left out.

this Pretty much proves it was indoctrination

heres the thread

http://www.escapistmagazine.com/forums/read/9.354425-Bioware-allows-the-release-of-The-Final-Hours-of-Mass-Effect-3-a-tell-all-app-for-2-99-WTF#14074722

As for Star Gazer, it could be a race in the next Cycle, but still: Shepard fails if he/she picks 2 out of the 3 possible endings. Why would Star Gazer be touting the heroic failure of an ancient being who tried but ultimately never stood a chance against the Reapers? Yeah, it's a fun story to hear about how Shepard stopped Saren and the Collectors, but ultimately those are non-points considering that he/she essentially only won 2 battles but got his/her ass kicked when the real war finally arrived. Not really a legend of a grand savior that people would pass down. Beyond that: I'm pretty certain that the Star Gazer mentions something about peace being achieved thanks to Shepard no matter which ending you pick. I could be wrong on this though, don't remember every line from that scene, but yeah, Star Gazer is the big fat elephant in the room to the Indoctrination theory.

There's one thing you're forgetting. At one point Liara comes to your room and says she's been working on something to leave behind incase you fail and she asks you how you want to be remembered... It could be that the next cycle has discovered this information cache and perhaps even beat the reapers themselves.

"Could be", indeed. Then again, it could be two human descendants talking about how Shepard saved their species. We've once again fallen into the realm of speculation. There's no way to prove that Star Gazer is a surviving human or a surviving member of the next cycle, though the evidence seems to lean towards the former.

The fact of the matter is that the ending is just a huge mess due to what Hudson butchered out of it. There's no way to prove it one way or another and apparently that was the original intention, but there was much more evidence to support the Indoctrination theory which sticks with the theme of the rest of the game (James mentioning a strange humming sound, and of course if you didn't know Shepard was at least partially Indoctrinated after that first dream-sequence then you're just not paying attention to what's been said about Indoctrination in the previous two games, particularly ME 2). However as I mentioned in the topic of mine that I linked a couple posts back, the butchered up ending ruined any chance we had for getting answers, or at least a stable theory with no holes in it. I fully agree that the Indoctrination theory is very sound, ALMOST everything fits, but Star Gazer is a big middle-finger waved in the face of the theory. He's the loose end that just doesn't fit.

I agree that some speculation is needed. but speculation is different from plot hole. It could be a new species, yes. But within the literal interpretation of things a lot of it simply COULD NOT be. We have one theory with a part not fully explained, and another with parts that are just plain wrong.

 

[karkar]

The points made in the article are are valid, and it is not as "crazy" as many people would believe. Vega's line about the buzzing is especially convincing. It's difficult to falsify it with any other explanation for why it was included, as it is suspiciously different than most of the crew's idle dialogue. Everything else in the theory appears to align with indoctrination symptoms, making a case that is difficult to dismiss.

However, I'm still not convinced...at least not entirely. Firstly, while the facts in-game hold up quite well, Bioware's actions since the movement against the ending simply don't add up. Just today they announced that they are at least considering providing a different ending. From what I've read, they have made NO public statements acknowledging the indoctrination theory. The unfortunate fact is that if people collectively decide that ME3 was a bad game due to the ending, there are going to be lower sales. Seeing as those in defense of the ending are outnumbered by those who disliked it, anyone who is on the fence about buying it will likely be more influenced by the latter group. If the game's team TRULY constructed this ingenious, thought-provoking mindfuck of a story, why have they not even hinted at their intentions to ensure that more people buy ME3? With the unpopular view of EA and many fans' reluctant boycott of ME3, some positive PR wouldn't hurt right now. They could have at least subtly acknowledged this theory without spoiling anything if it was their true intention, but their actions have, thus far, shown otherwise.

Secondly, if this was Bioware's "master plan", I think it was executed quite poorly. It is one thing to construct a subtle, intelligent narrative that some people may not be able to truly grasp, but it is another thing to only drop enough "hints" for a minority of players to construct their own theory. There is just barely enough evidence to make the indoctrination theory even remotely feasible, so why not make it just slightly more apparent what the actual outcome is? One would assume that the developers of a popular franchise like Mass Effect would want the maximum satisfaction from the maximum number of players, so it's unlikely that they would just barely make apparent these vital story elements that would be absolutely necessary to truly appreciate the ending.

I think the main reason that I am tempted by this theory is because I LIKE it. It's unexpected, different, and most importantly, it has the potential to be a hell of a lot more satisfying than the literal ending. The fact is, however, that it IS desperate. From any angle, it's incredibly difficult to see the signs of indoctrination, beat the game, and sincerely applaud the writers for a job well-done...at least not in its current state.

This is why I'm in favor changing the ending. I think ME3 is a fantastic game in most areas, and I thoroughly enjoyed playing it. However, the ending just doesn't seem right. I love the ME series, from the first time I played ME1 in 2008. Four years is a lot of time to form attachment to a series and its characters, and I don't feel that the current ending does them justice. I would like to see either a more "traditionally" satisfying ending or a more clear indication that the indoctrination theory holds true. Until then, I will continue to support the movement for change, and I will do so with as little "whining", "complaining", and "entitlement" as possible.

 

[RuralGamer]

As far as I'm concerned, the indoctrination theory sounds just as crap; basically, Shepard lost, the Reapers have succeeded, the end. All your actions were meaningless and the cycle continues. Talk about depressing.

 

[Da Orky Man]

snip

Yes, it explains a lot of things, but it opens up huge plot holes. For example, if you get a really low War Asset score, you ONLY get presented with the 'Destroy' option. So, why would the Reapers only give you the option to destroy them, and no others? It makes less than zero sense. Also, you only get the 'Synthesis' ending if you get over 3000 War Asset score, indicating that it's supposed to be the rarer choice. Again, makes little sense.
Another point is the Stargazer scene at the end. You get it no matter which decision you make, so it stands to reason that all choices prevent the Reapers from killing everybody. This again conflicts with the Indoctrination theory, since two of the options should lead to defeat.

Now for the second part.
The literal interpretation of the ending makes little sense, and is therefore not a good ending. The Indoctrination interpretation does fill in a few holes, but it makes others and also makes little sense.
So far, Bioware have had little to say on the matter. I currently hold ME3 as one of the best narratives I've ever seen, read or played. I'm not nearly as bitter as many. But they still messed up the ending. We wanted closure, rather than space magic and wild theories.
Appreciated if you could actually respond to this, as well as edit the OP to include the ploholes I mentioned.

Lol, this came up in the post above.

If you've got a really low war asset score the Reapers don't need you indoctrinated. They don't fear or respect you, and are not actively trying to indoctrinate you. Hence the fact that it's easier to break the thrall.

Again, there is absolutely no evidence that the Stargazer scene involves humans. Information and even species can survive the cycle, and as another poster pointed out Liara is storing your story on a device, in case you fail. It could be during the next cycle. Even in one there were rumours of the Reapers which survived from the Prothean cycle.

Since this causes no problems I can't see them as plotholes.

Edit - the fact that it was such a good narrative is what made me suspicious. These errors are not small, or minor, or anything. They're huge problems. People really believe Bioware, famous for this story and the detail in it, would suddenly make a million huge mistakes, RIGHT after getting hit by Harbingers beam? Don't buy it. A mediocre ending I'd understand, but not a broken one.

So, in order to get the second-best ending, you have to suck at the rest of the game? That sounds somewhat suspicious. And true, these isn't any proof to show that Stargazer is actually human, but really? When the fans have to construct such a theory that it involves the worst players getting rewarded, the better players being punished, the epilogue actually being aliens rather than humans, Bioware really did make somewhat of a mess of the whole thing.

However, I am rather happy that you answered me. That alone gives you more credibility than those who just ignore everyone else's opinion. But I digress.

Should I have a free reign in explaining it literally, I could go like this:

TIM was aboard the Citadel because he fled there, intending to activate the Crucible to take control. You an Anderson made it there because your armour was essentially destroyed, so the Alliance couldn't track you, so they though everyone was dead. Joker ran away because, really, a single frigate, without any support, in a battle with dreadnoughts all-round? he wouldn't stand a chance, so he retreated to act more of a command-centre, much like the Alliance intended if you read the Codex. So, when said coloured light was approaching, damaging any ship in the way, he tried to save the Normandy by fleeing.
The squad end-up on another planet because it was the only place they could land with roughly half an engine left, it being a garden world being left to chance. The mass relay explosions don't destroy the galaxy because all their energy is used in projecting the multicoloured light. And the extra scene is simply because that was the one ending where Shepard was told he wouldn't definitely die, it was just implied.
Oh, and the Catalyst was just that. The Catalyst.

There, all explained. Not very well, of course, but as well as any explanation as I've seen for the Indoctrination theory. Now, if the epilogue was different for the different ways of putting Shepard in the thing Liara made, I'd be impressed.

EDIT: And why are we so sure that Joker was in a relay anyway? Practically all the depictions of mass relays, especially in the novels, say that they're more or less instant, not continuous.

 

[RJ 17]

Snip

Which brings us full-circle to what I originally said: I used to be in the "it really happened" camp but not anymore, but since your OP was asking "What doubts are there to the Indoctrination theory?" I felt I had a couple to offer you from my previous way of thinking.