I'm so late to this party that I just wanna see if anyone's still alive...
Regardless, I feel like adding my own two cents to this already-overflowing penny reservoir.
I propose my own idea:
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The Catalyst Theory
(No offense to all of the FemSheps out there, but I’m just going with a generic male Shepard for the sake of specificity.)
Throughout Mass Effect 3, you are being indoctrinated in the same manner as those who went before you, through the influence of the Reapers:
Reaper indoctrination is an insidious means of corrupting organic minds, reprogramming the brain through physical and psychological conditioning using electromagnetic fields, infrasonic and ultrasonic noise, and other subliminal methods. The Reaper's resulting control over the limbic system leaves the victim highly susceptible to its suggestions.
Organics undergoing indoctrination may complain of headaches and buzzing or ringing in their ears. As time passes, they have feelings of being watched and hallucinations of ghostly presences. Ultimately, the Reaper gains the ability to use the victim's body to amplify its signals, manifesting as "alien" voices in the mind.
Indoctrination can create perfect deep cover agents. A Reaper's suggestions can manipulate victims into betraying friends, trusting enemies, or viewing the Reaper itself with superstitious awe. Should a Reaper subvert a well-placed political or military leader, the resulting chaos can bring down nations.
Long-term physical effects of the manipulation are unsustainable. Higher mental functioning decays, ultimately leaving the victim a gibbering animal. Rapid indoctrination is possible, but causes this decay in days or weeks. Slow, patient indoctrination allows the thrall to last for months or years.
And then the Catalyst upends everything… or maybe only reveals it. The Child is a Being of Light, and these Beings of Light, uncovered on the planet Klencory, are out to keep the universe safe from some vague “greater evil.” Here is the Mass Effect codex entry:
Klencory is famously claimed by the eccentric volus billionaire Kumun Shol. He claims that a vision of a higher being told him to seek on Klencory the "lost crypts of beings of light." These entities were supposedly created at the dawn of time to protect organic life from synthetic "machine devils."
So here it is: Indoctrination is just the Catalyst using the Reapers’ high-tech hypnotism capabilities for its own purposes. The Beings of Light aren't gods; they still have to use tools to accomplish certain feats. Reaper Indoctrination is the gateway that the Catalyst uses to begin asserting itself in Shepard's mind, ultimately trying to take him over for its side. It wouldn't be possible to just convince Shepard, we all know that; it had to be subliminal. The Catalyst is trying to convince with Shepard while the Reapers are trying to indoctrinate him.
They are designed as dual fail-safes.
So let’s put two and two together.
The Catalyst’s original plan was to keep creating Reapers out of civilizations as massive super soldiers to help him combat the Machine Devils if they ever reared their ugly heads, but he knows that the time has come for a change. His solution is failing, just as he himself admits. Thus, he has come up with another cure-all: Synthesis.
As the Reapers work for the Catalyst, they line up with his goal of uniting synthetics and organics to avoid the coming of the Machine Devils. We also know that the Reapers support Synthesis, as shown in Sarren of Mass Effect. When he became indoctrinated, Sarren was obsessed with the combining of synthetics and organics to create the perfect life-form. This can also be seen in all of the husks, which combine technology with the bodies of organics to create soldiers to serve the Catalyst.
The child from Earth was the Catalyst, using the slight indoctrination that the Reapers have managed to affect Shepard with in order to slip into Shepard’s mind and prepare him for his final decision. The heart-wrenching ordeals that this boy puts Shepard through are designed to make Shepard’s iron will falter, allowing the Catalyst more intimate access.
Shepard is the key to bringing this about. He has been the most influential being in the galaxy throughout the entire series. The Reapers would want him because of this.
He brought every species of the galaxy together and made all of the vital decisions of the time. He is an icon. He is a leader. The Catalyst would reason that, with Shepard’s face, it could convince people that Synthesis was the right path. Thus, if Shepard chose the Synthesis option, he would be convinced of this means and bring the galaxy along with him.
In Shepard’s dreams, the Catalyst is trying to keep Shepard focused on his failings and his inability to save the helpless as the Reaper indoctrination takes its toll in the form of shadowy images—eluded to by the Rachni Queen in Mass Effect—and in the tendrils at the edges of the screen that are seen in the control room struggle. While the Catalyst runs deeper into Shepard’s mind, it shows itself burning up to reestablish Shepard’s sense of failure. Eventually, when the Catalyst reaches Shepard’s subconscious and tries to win him over—when Shepard hugs the child,—his subconscious uses the fire image again to show that the Catalyst will lead to Shepard’s undoing.
The ending to Mass Effect 3 makes no sense if Shepard is awake and operating in reality. There are too many issues that are not addressed. How does Shepard survive a tank-busting superlaser blast with a limp and a bloody nose? I mean, really?
Why does Harbinger retreat from the beam at all, if it is truly the only way to defeat the Reapers? What else could he possibly need to do? (It makes no sense for a computer-based mind to make such a gaping logical error.)
How could Anderson beat Shepard to the control room when only one path existed? You see only one walkway leading to the control platform, and it is yours. Anderson was walking to the platform as you did, but he wasn’t in your hallway.
Why did Shepard have the bullet would that he inflicted upon Anderson? He was never shot there, but it makes sense if it is metaphorical. His mind is merging his will with the un-indoctrinated part.
Why did Shepard’s radio work with his suit torn apart? I still don’t get this part.
Also, while walking to the beam, trees of the same motif as those in Shepard’s dreams are visible when they were not there before, hinting at a link to the indoctrination and the Catalyst. This is a deliberate link. What else could it be?
Thus, at the end of Mass Effect 3, Harbinger’s laser spares Shepard, leaving him in a comatose state. This makes way for the final stages of his indoctrinating, which are to be seen in the conflict between Admiral Anderson and the Illusive Man. These are the two sides of Shepard’s psyche, with Anderson representing Shepard’s resistant side and the Illusive Man representing the indoctrinated portion. When the Illusive man is killed, Shepard defeats the indoctrination and, by doing so, truly defeats the Reapers; not just on a physical plane, but a mental—almost spiritual—one.
It's the ultimate victory… but he’s not out of the woods yet.
This turn of events suits the Catalyst’s plans much better, as is shows Shepard to be an incredibly strong-willed specimen, and, after final choice, one who thinks he is a willing convert—if all goes well. They could have his husk to use as living propaganda. If Shepard chooses to Synthesize all existence into a biotech hodgepodge, he willingly becomes re-indoctrinated, thus becoming convinced of the Catalyst’s ideals. While he begins to wake up, he sees the Catalyst’s vision of life in the biotech universe, narrated by EDI due to her synthetic-yet-human nature. In reality, it is the Catalyst singing a lullaby to its newborn husk.
The polar decisions—control and destruction—are both failures in the Catalyst’s eyes, with control being only slightly less of one. If Shepard chooses to control the Reapers, he is subconsciously reverting to the Reaper Indoctrination but rejecting the Synthesis option that the Catalyst desires. Furthermore, Shepard chooses to dethrone the Catalyst, which makes him a threat. This leaves the Catalyst with the options of a full indoctrination or termination, neither of which will leave the player with anything like a happy ending. As Shepard slips away, he becomes one with the lie that he is a Being of Light and is convinced that he was right, just like any indoctrinated being would be. It’s a sad, psychotic ending for our hero.
At both of these endings, Shepard’s eyes become cybernetic, like those of the Illusive Man and Sarren, symbolizing his fall to the machines.
If Shepard chooses the destroy option—otherwise known as the right option,—he rejects the Catalyst and the Reapers, imagines the fate of the galaxy based on what he thought he did—using Hackett’s voice due to its straight-and-narrow, steady-the-helm connotations that the Admiral exudes throughout the series—and awakens fully in control of himself. This explains why you can only get the Shepard-takes-a-breath clip from that choice, and we have no idea what awaits.
Now, this breathing scene is vital. How could Shepard blow up the Citadel, fall all the way back to earth, landed in the concrete rubble of London, and managed to survive? He died from reentry in Mass Effect 2, if you’d forgotten, and it's not something you can get better at with practice. There is no possible way that he was actually on the Citadel, regardless of any other explanations. Dreams always try to validate themselves, but they are easily seen as folly when one wakes.
Now, what happens to the Crucible in reality? When Shepard’s War Assets are as high as possible, they manage to push back the Reapers without him—giving him enough time to fight the indoctrination in his mind—and activate the weapon. If the player chooses another ending, Shepard would no longer want this, so it does not come about in order to keep the player’s choice integral to the fate of the universe.
So, when Shepard wakes up—if he wakes up—the war with the Reapers will be all but over… and the threat of the Machine Devils will create an even darker reality, leading to more games, probably set long in the future, when society has advanced enough to warrant their attention.
I'm swimming up a waterfall here, I know, but I truly believe in these people. I cannot imagine why they'd end it how they did, even if it was to kill the series. I'm a writer, and I'd never do that to one of my books; plus, with all the foresight they've shown, it's hard to think they just dropped all the clues and plot holes leaning that way on accident. If it’s just leftovers from a past story idea, why weren't they cleaned out?
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Feel free to search for holes in my reasoning; any refining ideas are very welcome.
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the original most kickass weapon in the known universe, the RYNO
