I am of the Hallucination theory you may have seen gabbed on about in other threads.
The whole game Commander Shepard was getting more and more stressed, as time went on she became less and less 'human'. In a way.
When you first get onto the Citadel it feels like a dream. You're crawling through a hallway of your own dead. Mysteriously faced with the Illusive man with no hint at how he got there. When he commands you, you put a bullet in Anderson and are using all your might to resist.
The bodies are like the phantoms in her dreams that she'd been having. They didn't seem real. Her mental state is weakened by blood loss, consistent exposure to indoctrination. They might not have even been real.
Let's use other examples of other people who'd felt it.
Saren said Indoctrination was subtle and crafty. The Illusive Man didn't even know he was indoctrinated unless you Paragon'd the HELL out of him. Rana Thanoptist (Get out of here before I blow up Vermire Girl.) who had a weak mind committed suicide after even her relatively small exposure compared to Shepard. Shialla (Green Girl) was only freed from it by the effects of the Thorien and was Mindlinked to the Feros Collenists who made a suprising effective force. I believe Shialla's mind-link allowed other's minds to stabilize and counter re-indoctrination, that and the exposure to the Thorian's mind.
Shepard in the dream chases the kid, a dream that started as Post Traumatic Stress from watching a kid die, a cross of guilt to bare. But as the game went on Shepard kept being exposed to the Reapers more and more and more, destroying them, getting close. Others even with no reapers around were getting taken over and killing each other.
In the dark dream Shepard is warned, as she runs chasing the phantom she sees herself hugging the child, smiling creepily as they both burn, a forewarning of what lies ahead. That the reapers are riding on an image of her guilt as 'The Catalyst' of her indoctrination.
"Good Endings." -
Finally Shepard stands at the end face to face with her nightmarish guilt. Having made it so far only through the will to beat the reapers. She is offered three choices by the Catalyst.
One is to Control the Reapers, to become them. However as I was hinted, she is indoctrinated herself in the final throws. This destroys the Mass Relays and causes the reapers to withdraw.
Second is the Biomerge of Technology using her as the Palate. Everyone in the universe is made into a Cyborg. Including Synthetics who are Augmented with organic. The Reapers Withdraw.
The Last is to carry on strong, We win or we die! You destroy the reapers once and for all. However the cost will be the death of the Geth (Who would willingly make the sacrifice to save organics if you persuaded them.) and EDI (Who was always ready to die to help Shepard.)
The Catch 22.
I theorize the Catalyst ISN'T what it seems. It the Catalyst of Shepard's Indoctrination. That in each ending Shepard does not die a true death.
Ending 1 and 2, Shepard's mind is overthrown, Shepard is indoctrinated and is now controlled, Shepard thinks (S)he is dead. Now a tool of the reapers who is still alive. The Mass Relays are gone, but the reapers are infinitely patient and truly unknowable.
The Illusive Man's path of control means Shepard didn't stop the reapers and now the universe is stuck without the Mass Relays and the reapers are infinitely patient.
The Biomerge Path, means all life has been given the ideal form for indoctrination of all. Shepard's indoctrinated energy is in all life, organic or not. And the reapers are a part of everyone now. Allowing them to begin a mass indoctrination beyond scale.
The Destruction Path, Shepard destroys the reapers. Overcoming the indoctrination. Waking up amidst the rubble on earth. (Shep is a sturdy SOB to take so much damage.) The Indoctrination attempt failed Shepard's conviction held through to the end and even in an unstable condition Shepard was able to hold to "We fight or we die."
Both other endings Shepard stops fighting and sees Her/Himself die. Stop fighting and die.
However is Shepard dead? Or is Shepard walking indoctrinated while the true ending is under design?
"The Bad Ending" -
Shepard quickly before everyone is ready, before the Crucible is perfected rushes to fight the reapers. The Crucible is incapable of the Technomerge and Outright Indoctrinating Shepard isn't an option.
With some Resistance left (Due to shorter exposure time) Shepard destroys the reapers, the unfinished Crucible destroys the planet, the reapers, everyone on earth and Shepard. Shepard never gave into the Indoctrination and was too strong at the time to ever do so. Too much resistance left.
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The Joker Vision
A final glimpse at what is going on, Joker crashing down somewhere. Is it a vision to placate Shepard? Is Joker lost and stranded with a need to be picked up?
The Reapers died, but so did the earth.
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The Possible Future.
"Can you tell me another story about the Shepherd?"
At some point Shepard is required, if (s)he is indoctrinated (Blue/Green) Ending. She awakens to learn the reapers are still out there. That doom is still upon them. And that through the sacrifices of others His/Her indoctrination was broken.
If Shepard destroyed the Reapers, Shepard awakens. Having destroyed the Reapers and fought off the Indoctrination. The Reaper Tech is gone. However Shepard is alive. (Shepard is very largely Cyborg, grey muscles, wires, AKA Lazarus Project Cyborg.) Meaning that the Geth also possibly survived.
The new Mission Either way involves coping with the change to the universe. Tracking down the lost. Picking up the peaces and building a new path.
"I need to find my people.", "I need to know that (Love Interest) is okay." At your side you have your people. "I need to get the Quarian's Home." "Wrex's Family needs him." "The Asari need to return to Thessia."
"We are all together now, our enemy is gone, but we are stranded away from home. We need to rebuild, but we, all the people of this Galaxy, stand together to rebuild. We will do on our own what we always have. We will forge our own path."
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