Shepard's Indoctrination: The True Mass Effect Ending?

Many fans were up in arms about the ending to Mass Effect (ME) 3, and with good reason. After three games of creating the universe as you see fit by making the decisions you want to make, the game takes away that freedom at the last moment.

In the last scene, Shepard, aboard the Citadel is confronted by some sort of God-Child, who is the Catalyst. The Catalyst explains that it created the Reapers to destroy organic life every 50,000 or so years to prevent synthetics created in that cycle from killing the organics. The Catalyst presents Shepard with three choices: 
1. Destroy the Reapers and ALL synthetic life (Destroy)
2. Take temporary control of the Reapers and force them to return to dark space forever (Control)
3. Combine both organics and synthetics together, making all life in the universe a hybrid between the two (Synthesis)
And that’s it. Just those three. Which raises a big question: WHY? Why did the Catalyst create the Reapers (which are synthetics) to kill organics to stop synthetics from killing organics? Why does Shepard accept these three choices as his only choices? Why did Shepard go around the galaxy collecting War Assets when it barely changes the ending? Why doesn’t Shepard say “piss off” and fight the war on the galaxy’s terms, not on the Reapers’? Why are there so many plot holes in the ending cutscene?

It all boils down to one answer: It never happened.
Let me explain: a new theory which aims to ‘fix’ the ending of ME3 has been gaining support on the internet; a theory based around the idea that Shepard is indoctrinated.
Here is a fairly “quick” and “simple” breakdown of it:
At the ending of ME1, it is revealed that Saren was indoctrinated the whole time, but was led to believe otherwise by Sovereign. This same thing was happening with Shepard; due to his many interactions with Reapers (talking to Sovereign on Virmire, being in close quarters with Reaper controlled Saren and the Collectors, the time spent in the Derelict Reaper getting the IFF, being in contact with the Reaper artifact in the Arrival DLC, fighting the Human-Reaper Larva in the Collector Base, and fighting numerous Reapers and Reaper forces in ME3) Shepard was slowly indoctrinated by the Reapers and it all culminates during the final battle.

During the last part on Earth, Shepard and the Hammer forces are running toward the beam that will transport them to the Citadel, but they are wiped out by Harbinger (yes, that is Harbinger that hits you with the laser). At this moment, reality stops. From here on out, everything is in Shepard’s head.
The conversation between Shepard, Anderson, and the Illusive Man is actually a battle in Shepard’s mind between the indoctrinated portion (Illusive Man) and the part of his mind resisting the process (Anderson). When the Illusive Man kills himself, this is the Reapers trying to trick Shepard into believing he has won. Shepard then reaches the Catalyst, which looks startlingly like the boy he couldn’t save on Earth and is presented three choices by the Reapers. The Control and Synthesis endings are actually the bad ones. These represent Shepard giving in to the indoctrination process, as evidenced by him dying in the final cutscene. However, the Destroy option represents him fully resisting the process and regaining full control of his mind.

You’re probably about to ask a big question: what makes me think this is true?
This theory ties up all plot holes that are made in the final scene, since none of it has to make sense, as it isn’t real.
The Normandy escaping and crash landing on a distant planet, with Joker, EDI, and your romance option emerging from the ship? False hope planted by the Reapers.
The gunshot wound inflicted on Anderson also appearing on Shepard, despite the player never seeing him get shot? His mind reflecting that fact that he is fighting himself.
The Catalyst looking like the kid Shepard couldn’t save on Earth? The Reapers trying to appeal to Shepard by using an image which conjures up guilt for him.
Shepard waking up in a pile of rubble on the ground (Destroy option), even though he was just on the Citadel in space? Shepard waking up after his internal conflict while still on Earth after being hit by Harbinger’s laser.
The Reapers creating a transporting beam that conveniently leads right to the control panel that can destroy them? A trick, to lure Shepard into a false sense of security.

So, what does this entail for the future? Hopefully, this is the ending Bioware intended, with the Destroy option allowing players to continue into the upcoming DLC, which hopefully encompasses the final battle.
I originally imagined the final battle to be a mix of ME1 and ME2: up in space, the galactic fleets are fighting the Reapers, like in ME1, and Shepard and his crew must fight to save the day on Earth, similar to ME2. This is where everything comes together and where it should lead.
This means that every choice the player makes actually has an effect on the game. Collect enough War Assets and the galaxy can beat the Reapers and Shepard can win the battle for Earth.

Here is a link to the video which provides a lot of support:

Understandably, this was a long post, but it means that the future still has hope. Please feel free to comment or PM me messages, but keep a level head and don't go off the deep end over a video game.

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