This theory takes in to consideration not only the events that transpire within the game, but sociological aspects and real world historical considerations that seemingly are relevant.
The theory can be summarized with the following title:
Borrowing Space Jesus from Babylon 5
AND/OR "The last temptation of The Shepard"
The ending to ME3 is so subtle, yet so easy. People fail to grasp it because on multiple levels because they could never conceive the ending would be this way and through their own arrogance essentially demand that THE ending be THEIR ending.
Thing is that is not the ending and by putting ones personal experience ahead of the canon it obscures the truth they do not wish to see as well as the one they refuse to consider.
The ending is simple. Shepard fails.
It does not matter which ending you chose, the "resolution" to the events in the game still come out to being the same. Completing the game is a fail state.
This elaboration will take a lot of description, but what we see from this is that in essence this makes this arguably the greatest ending any video game has ever had if true. In part because of how oblivious the general populous was to it, and in part because of what it essentially references.
Now I have to wonder if the devs actually were thinking this deeply, but technically the conundrum presented by the ME3 ending, Control, Destroy or synthesis is invariably one that hearkens back to the very root of all biological existence. At one point, proto cells had no method of which to propagate and pass on genetic material. We know from modern biology that viri are not living things but they do possess the ability to propagate themselves. It is hypothetical cellular theory that the origin of biological life comes from proto viri infecting proto cells creating a synthesis of both virus and cell capable of perpetuating life, thus we see what was born of that synthesis. Obviously there are mirrors to how the ME story plays out to this theory, but it is questionable if this is in fact the core of the narrative. Regardless we do in fact find there are parallels, be them intentional or not.
So before we get into what is the true meaning of the ending, we will first start with "which" is the canon ending. The intended canon ending invariably would have to be the "red" ending. Arguably on multiple levels the most "downer" of the endings. Now even early on we have to touch base with the fringe theory of "Indoctrination theory" which is a real part of the ending however the indoctrination theory "stops short" of what the ending truly is.
Let us review. The final mission begins, Shepard eats a face full of Reaper beam as everyone is blindly charging the citadel. When Shepard "wakes" from that point on everything becomes "other worldly". Fuzzy distorted vision as you limp onward toward the beam, despite you hear radio claiming the strike team is defeated and calling for retreat. Shepard walks toward the light and he is only interrupted by one inconsequential marauder.(technically the final boss)
Shepard makes it to the beam and the load screen is a beaming tunnel of light ascending upward to the citadel. Now, when he arrives what do we see? A citadel that has no resemblance to any part of the citadel ever known, filled with corpses and strange quadruped aliens who have essentially never appeared before now who ignore you and work the machinery.
There is the point also that is brought up in IT that Andersen somehow gets ahead of you and as you walk forward you enter into even more never before seen parts of the citadel. What all of this entire scene is is in fact Shepards near death experience, but in this experience Shepard still has the means to survive as his survival is actually more important than he or anyone realizes.
The encounter between Andersen and The illusive Man is essentially the Angel and Demon on Shepard's shoulders pushing him toward what his humanity perceive as right and wrong. However none of this is in fact real. We know this because there is no logical reason for TIM to be at this location, and there was little or no likelihood for Andersen to have made it to the Citadel. Invariably Shepard is forced to side with Andersen one way or another and move beyond this confrontation. Specifically after Andersen is shot, Shepard blacks out again, but while still in death throws responds to the fleet hail with "What do you need me to do" and collapses in front of the pad ascending to an entirely new level.
Another unknown unfamiliar part of the citadel Shepard is now on "Star Child"s level. Star Child presents Shepard with three choices. In these choices we must look at Star Childs reaction to Shepards Choice. In Control, SC watches as you take control. In Synthesis SC resistingly vanishes however if you chose destroy, you continue the fight. This is why later in the ending you see Shepard take a breath under the rubble. SC Immediately vanishes when you chose destroy. The reason is, the Star Child IS indoctrination. The Indoctrination began in key points after leaving the citadel by forcing Shepard to Chase it in his dream like state. If you chose control, The reapers successfully have indoctrinated Shepard. If you chose Synthesis the Reapers still win by becoming one with organic life and their survival is continued. However if you chose destroy the indoctrination fails and Shepard is cast out of the indoctrination at the point where he was taken in at just after the face full of Reaper fade to black.
Now so far this has been predominantly just an explanation of Indoctrination theory. However the most important part is in fact where the similarities exist in "the ending". The point people loathed most about ME3 is how all 3 endings were virtually identical. What people fail to understand is how important that is. What are the key elements to the ending? Shock wave emitted through the mass relays, destroying them in the process. Joker failing to outrun a shock wave, Stranded on a planet with two moons. This forgoes the EC ending for the moment. Now through repetitive tropes we know that typically when something in fantasy/fictional narrative "rewrites" history or existence it is often represented as a outward expanding wave. This is what we see in all three endings. The Shock wave rewriting existence to represent Shepards decision upon the cosmos. The crash of the Normandy is the birth of the new form of organics as those on the Normandy will populate this new existence.
The last commonality is what ties these events together. One image. One adult, One child, Facing two moons. This is further reinforced thanks to the EC ending because the only additions presented by EC is the ability to question SC, Shepard refusing resulting in outright fail state but Liara being able to pass on additional info to the future of organics who as we see in this ending are descendants of the Asari and explains why in the EC ending the Adult/Child scene is replaced with two female Asari-esque voices instead of what the common ending showed.
It is in this moment we begin to understand the true meaning of the ME3 ending. It was said in every single ending "Tell me the story of THE Shepard." by the child in this newly created dual mooned existence. The story of Mass Effect is how this human "Sheparded" all life into a new era of existence. No matter the ending we see the progenitors of this new existence bred the strengths of all of the old existence allowing the sum to become greater than the individual parts that had previously failed. This revelation now forces us to backtrack and see everything that we missed that was telling us this all along. The Shepard is the icon of lore from generations past. Essentially the ending is a take on the bible. As we now move backwards to the beginning we start to see key elements that allow us to see these comparisons.
The conflict between Andersen and TIM is essentially "The last temptation of The Shepard" as it is the reapers final attempt to block Shepards progression within the Indoctrination. This is why TIM is noted for saying "I need you to believe". This was the reapers ultimate desire. To have what was the paragon of this cycles organic representation to willingly submit to the will of the Reapers.
From here working all the way back to the original Mass Effect we begin to see more and more religious context. From the more questionable notion that by the beginning of ME3, not including optional DLC squad mates, excluding those who are by canon identified as dead(IE Thane, Jack) and only accounting 1 char for certain players who invariably have to be decided upon (IE: Ashley or Kaiden, Wrex/Grunt) The total number of squad mates Shepard ends up having comes to 12(arguably 13 which is still within arguable parameters), Representing the "Twelve disciples"
We see other examples in how there really is no "good or evil" in the game. You are viewed as either Renegade or Paragon. This is represented in the way that Shepard never really sides with evil and at worst all you can do is make him into a Dbag with a bad attitude. His default state ends up being "good" leaning more toward being a paragon of good.
Beyond that we look at the narrative. Despite humanity being viewed by alien races as a brash upstart species, Shepard even from the early going is repeatedly viewed as "The only hope" and every time he has any doubt, he is encouraged because "So many are counting on him/her" How is it one individual from a highly resented race can somehow become, through the course of becoming a "spirit" as a specter ends up being viewed as "salvation" of the entire galaxy that races even trip over themselves to remind Shepard how vital his role. Then all too often it is Shepards role to lift up the spirits of his own crew who are losing faith. Many times we find Shepard being uncannily adept at dishing out insightful one liners that end up being uplifting quotations.
Even if you look at ME2 you realize that Shepard was "resurrected", a feat accomplished for one person, Shepard to which was accomplished via the "Lazarus Project" where he was brought back from the dead.
Honestly we knew from the very first installment that there was going to be heavy religious context in the game, Simply from the main characters name. You can call your char what ever you wish, but the game will only ever refer to that char as "Shepard" which hearkens back to biblical references of the Shepard of the lamb.
Now there are a few other loose references and ins and outs, but for the purpose of explaining what seems to be the hidden truth of the narrative this is sufficient. The ME3 ending serves as the end of the trilogy which in effect acts as a modern take on the New Testament where the player is playing a character that is the salvation of the galaxy in "The Shepard" who unlike in the bible failed in its objective but it is suggested that through his sacrifice helped to create a new cycle of organics that do in fact manage to best the Reapers and finally end the cycle once and for all. Its vaguely reminiscent of what was attempted with the narrative of and more accurately the ending of Babylon 5, where the primary character in turn becomes the "salvation" of the future for generations to come.
This is also why the general populous does not come to this conclusion. Most players hold the intent to play for "Their" ending, and make little or no effort to understand what was the "intended" ending. In bioware titles that are a part of a series, we can "learn" what the "canon" ending of one title is, by how an unimported game reflects back on the prior installment. We see this for example in ME3 where a "default" ME3 game with no import shows that "Jack" is listed on the wall of the dead on the Normandy from the earliest point you can access it. While Jack can in fact appear in ME3, the canon indicates that Jack in fact was one of the casualties (and from the narrative it is also logical) in ME2s suicide mission. The same is also seen in references in Dragon Age 2 regarding both Origins and Awakenings. So when players are more concerned about THEIR play through and the choices they made, they will not be as likely to pay attention to the narrative intent of the developers. (and this is why you should never import a save file that houses personal choices between games, Like the witcher, Bioware, ect as your personal choices end up obscuring what the "default" is)
Another reason why this was not seen by players is this current generation of gamer. We live in a generation where Christianity is being increasingly rejected by the general populous and younger generations embrace atheism. On one level it is the fact that many of these who reject theology were simply not exposed to many of the "stories" of Christianity, so the more obscure of them end up going undetected. On a much wider level, it never dawns on many simply because they do not want it to. With rejecting the ideas of Christianity to begin with, few would want to accept that they had been identifying with a "Christ like" figure. Even more threatening is instances where Shepard in fact mirrors religious ideologies that these Atheist players can in fact identify with, it makes it far harder to swallow when you realize these in fact originate from a source that many atheists want to think is a faith of nothing but exclusion, hatred, and anger in their unfounded preconceived notions
None the less, while there are still many details out there, this is definitely a very long elaboration to illustrate the idea. ME is a series that is a modern attempt at using the bible as a template of the story, but the "end" is that Shepard failed, but in doing so allowed future generations to succeed.
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Now the above theory was written quite a while back. However to give additional perspective to consider due to more recent developments. You can refute the "space Jesus" idea of ME3, but one thing that you seemingly cannot escape are the religious references from biowares products. For example, look at the rear box art from Dragon Age Inquisition dubbed "the last supper"
Again, similar imagry, Similar 12/13 "followers" all situated by the great salvation, of which you control.
While the theory may or may not be correct, there is an undeniable suggestive inference from Bioware hearkening to at least Christian ideology in the narrative and the emulation of iconography in its presentation. With such blatant referencing it is hard, if not possible in retrospect to not look back over ME through the perspective as it being written as sort of a retelling of the bible and other religious tropes, when seemingly they keep hitting people over the head with such references while still trying to retain some degree of interpretive subtlety. Again, the theory may or may not be correct, but it does pose enough questions to deem it worthy of consideration, of which it seemingly never even remotely dawned on the largest bulk of the populous regardless of what side of the debate they were on.
EDIT: With all that after all is considered, If this is in fact true I get the feeling that the underlying purpose of building the IP around this "space jesus" theme would have a lot to do with trying to use a futuristic setting, in order to convey the message that with this modern rejection of theology, that when you cut past all the literalism on both sides, science and religion are not and never have really been at odds, and those who put them at each others throats are those who stand to benefit and profit from said animosity.
IF this is in fact the real intention behind the franchise and the narrative it was built to express, given the venomous reaction to it essentially trying to crucify it, then it becomes an astounding instance unparallelled in gaming where myth meets life meets art meets life and it then must be considered for being arguably the greatest gaming story ever told.
But lets be realistic, Human beings are small, petty, unimaginative creatures with only rare glimmers of promise and potential. With something as complex, nuanced, subtle that would have required not only extensive collaborative effort, Unprecedented confidence from a publisher who hasnt been known for pushing boundaries or taking risks for decades, and unimaginable maintained secrecy in order to keep even staff working on the project in the dark to the true nature, the odds are seemingly very much against the likelihood of it being the case. However, despite the odds being against it, there are far too many questions this theory is able to patch up that the existing theories failed to accomplish and with a developer like bioware (even in their deteriorating state)
You have to wonder, which is more likely? an unimaginably ambitious effort that ended in flawed execution that was misunderstood by its audience? Or that a dev known and renown for its "quality writing" would flush out a half assed turd when expectations were at their highest, when there was really little or no rush, lack of resources or publisher interruption to point to as the reason for it, and the blame is laid at the feet of a small core of people, who decided to take the entire direction of a franchise out into left field from what they had spent two prior games crafting that franchise into something of critical acclaim? with no logical reason why they would willingly do that to a franchise these people had been working on for likely more than a decade to create.
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