Be warned: This post will be full of spoilers. For those of you that didn’t play the Mass Effect Series, move along. There’s nothing for you here. This is one man’s attempt to rationalize the perceived “shitty ending” to a large-scale gaming franchise. If you did play the ME series and you haven’t yet finished the game, do not read beyond this paragraph unless you want details.

That said, here’s why I think Mass Effect 3’s ending hides awesomeness among the bullshit most people seem to see.

I’ve read and watched a few theorists bring the thought of the “indoctrinated ending”. According to this theory, as Shepard is struck by Harbinger’s laser while running toward the Citadel transit beam, he is knocked unconscious. What follows is the result of Reaper indoctrination.
Before you throw this theory out the window, remember this: indoctrination is not conversion. Indoctrination is not what creates husks, brutes, banshees, etc., Reaper conversion is. The main difference between the two being that indoctrination is able to influence people to think the Reapers are correct in their motivation. Indoctrination is a tool to subdue the populous and make the job of the Reapers easier. It is also used to control non-converted beings.
Matriarch Benezia. Saren. the Illusive Man, the doctor from Arrival whose name escapes me at the moment… these people were not acting of their own free will the entire time. They believed that they were and each was brought to a realization of Reaper control and fought against it in their last minutes. Even Saren and the Illusive Man, though partially Reaper converted, could fight against indoctrination, ultimately deciding to end their lives rather than continue to serve the Reapers and the ultimate destruction of all organic life (a nice sort of full-circle scene from 1 to 3, if you took the Paragon options).
Back to the subject, indoctrination does not require any implantation or noticeable manipulation. Indoctrination is transmitted through a field given off by Reaper artifacts and, most notably, Reapers themselves via prolonged contact.

No, the Citadel and the Mass Relays do not count. Indoctrination is not necessary until the end of the cycle. The Reapers are too smart to pop that one too early.

Being that he was within close (Reaper relative) contact with Harbinger during the time of the blast and, as the screen went white, possibly knocked unconscious, this leaves Shepard off-guard and ripe for indoctrination. Also, it can be argued that evidence of indoctrination shows before this through the dream sequences and the little boy who Shepard can’t seem to forget. Some may even argue that Reaper-tech was used in Shepard’s rebuilding or that, due to his prolonged interactions with the Reapers and their agents, Shepard sees things that aren’t there or that the Reapers want him to see.
The theory continued that everything happening beyond the white out when the laser strikes was an indoctrinated vision wherein Shepard communicated with the Reapers and, as the defacto representative of all galactic civilization (including even the Geth and the Rachni if you played your cards right), Shepard is given, by the Reapers, the ultimate choice of the fate of this cycle.
Speaking with the Catalyst (who I’ll get to later), you’re given two paths (possibly three) meant to confuse you as the player. If you pay attention to what the Catalyst says and does, this is very apparent.

The Catalyst represents the “creator” of the Reapers and reveals that their goal is to wipe out all advanced organic life to bring order to the chaos of the galaxy. Shepard, uncharacteristically, listens with intent to the propaganda that his ultimate enemy is spewing. The Catalyst reveals that, at this point, two things are certain: 1. Earth will be spared, and 2. The Mass Relays and the Citadel will be destroyed. No matter what you do, these are inevitable. At this point, you’re given a blue path, a red path, and potentially a green path. Blue, as you’ve been lead to believe through three games, is the Paragon way to go, however, it allows the Reapers to survive and also elicits a suspicious expression from the Catalyst when this option is taken as he stays online enough to have Shepard look back and see him sort of smirk. Is this really the blue/Paragon way to proceed? Shepard “controls” the Reapers at this point and, because we all know what kind of guy Paragon Shepard is, he’ll probably manipulate them while he’s still able to reconstruct some of the mass relays and possibly even the Citadel. Happy ending, right? Space is still traversable, everything goes back to status quo.
Until the work is done. Given that the Alliance with all the help in the galaxy could construct the Crucible from nothing but some ancient-ass Prothean blue prints and raw materials in the span of, say, a month while Shepard’s out in space? Two months? Six, tops? How long is it going to take the Reapers, the most advanced synthetic species in anything ever ever, to rebuild the relays and their giant, live-in death trap? Give it a year or five… maybe.
Once the work is done, the Reapers disappear into Dark Space never to be heard from again… until the next cycle, 50k years from the end of ME3, when hundreds of thousands of generations have come and gone thinking that the Reapers would never return. 50k more years for Prothean markers to be further pushed into obscurity. 50k years without ever thinking a warning is necessary. So, the Reapers skip a cycle. When you’re an undying, nigh-invincible, gigantic machine race that can survive outside of the galaxy, all you have is time. By then, Shepard’s personality will be just another voice in the endless chorus of souls inside the Reaper enclave.

Then, of course, there’s the red/Renegade option. The indoctrination theory contends that, as soon as Shepard begins to do real damage to the power conduit that will destroy the Reapers forever, the Catalyst image fades away, almost as if it is upset with Shepard’s decision. This, in my mind, proves that what Shepard is doing in this sequence is right for the galaxy at large, but very wrong for the Reapers.
If they’re all dead, the Catalyst’s continuation of the cycle dies as well. What we see here is that Blue and Red have stopped being what’s good or bad for Shepard, the galaxy, and anyone out there fighting the Reaper threat. Blue has become what’s good for the Reapers, red has become their downfall. The only way that these choices would appear as such to Shepard would be indoctrination.

There’s also the matter of the green beam. The merging of synthetic and organic life which is referred to by the Catalyst. While you may read the above and think this is the happy middle ground, think again. This is just another Reaper trick to win. If synthetic and organic life forms are merged and balanced, the cycle is complete. Order is wrought from chaos per the Reapers’ MO and they leave Earth and pull out of the galaxy until the next cycle, but they’ll be back in 50k years to settle the score when shit gets out of line again.

If you have enough resources tapped and you take the “destroy” or “synthesis” options, you also get the little bonus scene of Shepard’s chest plate with the N7 dogtag gasping for breath in a pile of rubble.
You will notice, first, that this pile of rubble is made up of concrete and other clear pieces of decimated Earth city. Some contend that Shepard “fell from the Citadel” but I think that’s going a bit far. Shepard has survived a lot, but a plunge from upper Earth orbit back to the ground, landing on your back in a shattered cityscape and somehow not dying of suffocation or burning alive upon re-entry? Simply, no. Indoctrination while KO’ed in London is the logical fit in this instance. Oh, and the “control” option doesn’t get this ending because Shepard merged his consciousness with the Reapers, so he’s dead-dead-dead.

There are a few other details that support this. The fact that Anderson was “right behind you” yet somehow winds up on the Citadel FAR ahead of you, slogging through the same dark hallway you’re in, opening the same giant door to the same bright chamber you enter (without you seeing any evidence of light) and also Anderson’s general stature while working the console. He looked very robotic and strange while the Illusive Man moved as fluidly as he ever did.
Also, you’re running with your squad and they don’t show? You’re probably running with any weapon other than a pistol but it’s the only one you wake up with IN YOUR HAND ALREADY? Too much left undone. Too much missed. Indoctrination.

In conclusion of part one, the Indoctrination Theory holds some weight. However, I have developed an alternative theory based on the post-credits scene which seems to make perfect sense and also explains the fate of the Normandy after the blast begins destroying the relays.

The Grandfather didn’t know the full details of the end of the story. Plain and simple. This explains why things were nebulous and unexplainable. Everything that happened after the laser hit Shepard as he ran was all purely speculation or fabrication. Except the Reapers dying/leaving and the synthesis if you chose that option.

The history of Shepard is extremely well-documented within the ME universe. The Alliance has a file on him detailing all of his exploits. So does Cerberus. So does C-Sec and the Citadel Council. On that turn, all the Citadel Races probably have a copy of whatever file as well if not investigations they’ve done on their own. There’s also the matter of the logs of the Normandy and the Codex Shepard probably left behind in his quarters. Every element in all three games is logged, stored, and filed away in multiple places… except those last few minutes after the Harbinger beam hit.
The impression you get from the old man and the kid in the field after the credits is that this is a story to which “the details have been lost to time”. The details were probably very well known in generations prior. The details of the main portions of the game could have been accounted for in any of the aforementioned historical and accurate archives. There would probably even be the (disappointing) picture of Tali’s face stowed away in there if you happened to choose that romance. Proof. Evidence. Facts which have since become legend, passed down since the end of the cycle.
In order to get some closure to the facts and figure out what happened in those missing last moments of the Battle of Earth, people did what they always did when confronted with an unknowable question: made that shit up. Seeing as no one could know the full details except Shepard himself, they grafted on the ending as a way to close everything out. Illusive Man dies (possibly in a more noble fashion), Anderson dies (also in a noble fashion), and Shepard “dies” in the most noble fashion possible.
Much of history now is a misconception and remember also that history is written by the victors. If they were going to build a Shepard statue on Earth or Akuze or wherever to commemorate his defeat of the Reapers, people would want details of what happened and wouldn’t care if those details were slightly on the false side as long as it sounded awesome. And it did. And Shepard became a legend.
This also explains the wreck of the Normandy, who survived, and where they ended up. The Normandy could have been completely destroyed or never left Earth orbit but, in order for the Old Man to give some significance to the story for the Kid, he made the Normandy crash on their planet. You’re always more interested if it’s got something to do with where you live. It could have been a total fabrication or it could have been told to the Old Man by his own Old Man when he was a Kid. You don’t see the races of these people, though the voices sound decidedly human as far as ME voices go. Personally, I think the Normandy crash was part of the legend told by the Old Man, not the facts.
The facts were probably much more simple than your squadmates abandoning you and somehow getting to the Normandy in space without a shuttle or pilot and under heavy enemy fire and beating the beam through the Charon Relay. It did not take Shepard long enough to decide the fate of the Reapers to allow all those things to happen. It makes for a better ending when you’re telling a kid about it. If you’ve ever told a kid a story, you know how sad they get if people die. Sure, Shepard “dies”, but Shepard is the legend. You have to give them hope that the legend lived on through his friends, who happened to crash land on your home planet. It’s the Old Man giving the Kid something to fantasize about.
Given that the crashed Normandy had bunches of humans on it in order to propagate the species, we’ll assume that the Old Man and the Kid are, indeed, human. Do remember that asari can reproduce with any species and that Garrus and Tali (beyond making out on the gunnery deck before the Battle of Earth if you didn’t romance Tali) are both the same dextro-amino configuration and, since Tali has the Geth suit upgrades allowing her to soon be able to go without the suit completely, meaning we could possibly have half-Quarian/half-Turian kids running around somewhere. Showing any amount of little blue girls or crazy Russian-accent, flanged-voice, half-bird things would tip us off to the fact that this was, for sure, the place where the Normandy landed.

To summarize, no matter how you might interpret the ending, the simple fact is that another Mass Effect game, at least in the same era with the same characters, is probably not going to happen. Bioware confirmed (though, it wouldn’t surprise me if they went back on it at some point) that this was the absolute last ME game involving Commander Shepard. Even if you got the N7 chest-heave before the credits hit, I believe this to be true. They’ve already done the “bring Shepard back from the dead” thing, they’re not going to use that twice.
If the destruction of the Mass Relays holds true then you’ve essentially cancelled the entire space opera. No faster-than-light travel makes for a pretty damn boring jaunt around the galaxy. Based on the physics of the galaxy map, you’d run out of fuel before making it half way to the next system from Earth let alone Palavan or Thessia or, God forbid, Rannoch.

Was I satisfied with all my choices boiling down to three different colored effects? No. Was I satisfied with the ending overall? Sorta. Would it have been nice to have some more closure on my squadmates and the rest of the galaxy? Yes, especially considering that without the Mass Relays, you have a WHOLE lot of alien fleets chilling in Earth orbit after the Reapers go away/are destroyed. Granted, there’s a lot less people on Earth when all is said and done, so all those Turians, Quarians, Drell, Hanar, Geth, Asari, Volus, Elcor, and the Merc Groups from the Terminus Systems are going to have a place to stay and build a society. Earth just became the galactic melting pot from which there is no escape and I’m interested in how that will go down in the future. Maybe that’ll be the plot of ME4.

I hoped for more and I’m sure you did, too, but all the people who just didn’t get what BioWare was (hopefully) getting at as mentioned above are the ones railing against the wall and petitioning for a new ending. More closure would be nice, but if you take anything above into consideration, it might wrap things up a little nicer for you.
/end dissertation
Keep fighting the good fight.

—end transmission—