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After analyzing the first couple of games and finally going through the ending of ME3 a couple of times as well as from numerous forums i have poured over to satiate my empty feeling after completing my favorite series of all time, i have finally come to a conclusion. The last bit on the citadel in ME3 is indeed indoctrination and i believe that may have actually been Biowares design in the end. However i feel that Bioware quite poorly presented this and while the ending is good, it doesnt fit ME which has generated so many different and complex relationships and where the entire series is focused on your decisions. This is what makes this game an RPG, the impact of your decisions kind of like Fable although i dont compare the games. Also im angry at the Normandy part, that whole thing should just be cut, no reason why my crew should be onboard(how the hell would they have gotten there) and Joker should be fleeing(or whatever the hell hes doing) from Earth during the fight to save humanity, he didnt do that against Sovereign or the Collectors thats for sure. All in all what im trying to say is that the ending is good but it needs to be better elaborated on, should make more sense, and give closure to what you have accomplished throughout the series. Im hoping to hear from Bioware regarding this matter as they can no longer avoid it and maybe they didnt quite end the game due to the fact that it hasnt yet been fully released globally.

Hey, Mass Effect fanboy here, finished the game last night on paragon. I too was disappointed.

The idea that the end sequence is Shepard being indoctrinated is very interesting. It's very dream-like (as you say, hallucinatory) which would certainly suggest it is all in his head. It also smells right what with the direction the writers have seemed to be taking this thing. However there are some issues. If he's being indoctrinated now, why didn't it happen earlier? It's not like he hasn't come into close contact with reapers before. Also, what to make of the Normandy sequence? Is that in his head too?

I haven't been doing any research into the current speculation theories, but my initial reaction was that the star child was meant to be a transcendent being, call it God, Q, Singularity what have you, and it realized that if Shepard could get so far as to manipulate the mass relay technology that it had left behind, then it was time to give organic life a choice in altering the creation/destruction cycle it had created. Ooooooorrrr, I could be totally wrong because I am no smarter than anyone else.

In general, I thought the ending was seriously disappointing. It's like the writers got lazy or cowardly and so they cooked up something deliberately ambiguous. It is totally out of place with the rest of the series. Really a shame in my opinion.

I too found the ending to be quite miserable, amazing game in all other respects though. The problem for me is that they dealt with it way too quickly, I could come to accept the star-child and his choices if only I had had the time to ask him 5-10 minutes worth of questions. I would have also welcomed an epilogue seeing what becomes of everyone that Shepard has touched. It seems like an ending that wanted to be awe inspiring but instead turned depressing and lacking in closure.

The most shocking thing however is the destruction of the relays, both forma story perspective and form an IP one. It makes the story really depressing since civilisation as we know it can no longer exist. But form an IP perspective it changes the Mass Effect setting so radically that any new content set on that universe will feel not feel like mass effect. But I suppose that there can be some merit to that, keeps the series form becoming stale.

Also what of the whole "mass relays, when destroyed, explode like a supernova taking their system and anyone in it with them"?

Hey guys, so I spent some time going through the speculation theories and Hunter, I think I am starting to agree with you and the indoctrination theory. Partly out of desperation I admit, but also because I don't see any way to completely disprove it. It also allows for the slim hope that this is not the end! In fact the indoctrination theory is the only thing right now motivating me to complete a second play through.

O man o man o man I hope the theory is correct.

In case anyone isn't familiar with the theory I'll set out it's basic argument. Sorry if I get some of it wrong. There is also a pretty good fan video that explains it. Proof Mass Effect 3 Endings Were Indoctrinations - YouTube

1) From the moment Shepard goes down in Hammer Company's charge on the Reaper in London, he is out cold and in the indoctrination process is beginning.
2) The whole sequence of entering the Citadel, confronting Anderson and the Illusive Man are all in Shepard's head and setting him up for the final stage of the indoc process.
3) The star child is no more than the manifestation of a Reaper chosen for its sympathetic appearance. In order for the indoc process to complete, the Reaper must convince its victim that living in communion with the Reapers is possible. Therefore, if Shepard chooses the blue option (control the Reapers) or the green option (singularity of synthetic and organic) then he is allowing himself to be indoctrinated. The red option is the only way to resist indoctrination.
4) If done properly with a high enough Effective Military Strength, the red option will result in a "secret" ending that suggests Shepard may have survived the entire end sequence and is on Earth.

Note that the their is an odd contradiction with the blue and red choices. The blue choice, (controlling the Reapers) was the goal of the Illusive Man an indisputable antagonist throughout the series, yet it is presented as the paragon choice by the star child. On the other hand the red choice kills the Reapers (the indisputable antagonists) and yet it is presented as the renegade option! Is the star child/Reaper deliberately tricking the player over what choice to make?!

In case you haven't noticed, I have been going slightly insane over this.