I have seen the videos, read the codex, and seen the threads. The indoctrination theory, as interesting it is, discredits a lot of other factors and places a heavy emphasis on Shepard. I believe the whole indoctrination setup was meant to be a crucial factor towards the ME3's story and ending but was scraped due to leakage like the original endings, EA, or bad writing in story. Anyway, here are my thoughts about the indoctrination and ending issues that don't make sense to me:
1. The Clique: Our crew, squad, companions, etc. Those who were with us on missions involving reaper tech or influence (IFF, Virmire, etc.). Isnt it possible that they could of gotten indoctrinated? Could it be that the reasons why some characters acted the way they did was because of reaper influence?
2. The Tech: Citadel, Mass Relays, IFF, EDI, & Legion along with all Geth. If having any interaction with Reaper technology can influence someone can it mean that everyone in the game is indoctrinated in some way? The Citadel, Mass Relays, & IFF was all reaper tech while the Geth and EDI interacted with Reaper tech, whose to say that anyone wasn't indoctrinated if we're all surrounded by reaper influence. What if the reason why the Geth developed a sense of existence was because of one unit being influenced by a reaper that spread throughout the consensus?
3. Legion: Why is it that Legion is different from all the Geth? I understand some Geth are against the Reapers but why is it that only Legion is aiding us an not the other Geth? Why did Legion use a piece of our Shepard's armor to fix itself. Legion said there was a hole and needed to repair it but the hole is still there and it's obvious the N7 armor didn't cover it all up. So why use it? Part of me sympathizes for Legion but after giving it some thought it could be possible that Legion is really controlled by the reapers as an insurgent for the heretics or Geth.
4. Indoctrination: How does one become indoctrinated? An how does the technology of a Reaper influence indoctrination? I am looking for specifics as to how the reaper infiltrates and controls others. Is it like the way the Leviathan does it but only slower and subtle or does it use the human conscious to pressure the individuals guilt, passion, and aspirations and convince through dreams or hallucinations to do dangerous and extreme things to achieve or redeem success?
5. The Prophet: In ME1, on Eden Prime there was a Scientist that was going insane or crazy. What ever happened to him? Also what ever happened to everyone on Eden Prime? Sovereign was there so is it possible that his influence spread to the colonists?
6. The Reaper: Despite the Leviathan DLC, which I believe is crap, could possibly be part of the whole indoctrination theory an how meeting the species that created the reapers never really happened but was all a hallucination in Shepard's head. I know its a bit farfetched but why is it that a species so superior and possibly the first in existence itself not be able to contain the situation or simply made an off switch on harbinger? Why was it that they were not able to stop the Reaper extermination before it was too late? I believe it was all a hallucination. I think there was an ancient superior alien race that experimented with indoctrination to dominate future and fellow species that would soon evolve and use the indoctrination to make conquering the universe much easier with less destruction and chaos/war etc. They created a unique species superior in intellect in a lab and infused this species with heavy physic technology infused with element zero. They infused so much that the creature was able to indoctrinate an take over. The take over could of been out revolt, flaws in evolution seen, or because of the destructive potential power seen from element zero.
What do you guys think? I know its a lot but these are some of the issues I have with ME. Hopefully some of my questions can be answered. Thank you.





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