I just want to take a moment to thank everyone for their response. There's so much here to dig into, I really appreciate it. I'm very happy that people jumped in so quick and shows that ME has a solid fan base that really doesn't seem toxic.
On that note, there have been some things that are stuck in my mind that I'd like to explore. One, is the codex entry that explains that some indoctrinated can be used as, I'm paraphrasing, as signal amplifiers. I'm a computer/electronics geek so my thought is that it's like a repeater. The indoctrinated boosts the signal so it can go farther. Shepard was already a stand out in military circles, a polarizing force. Nihlus was there to scope her out as she was already a candidate for Spectre status. Her interactions with Sovereign, Saren, and the battle for the Citadel proved that she had unspeakable amounts of strength, vision, leadership, and influence. What if the Reapers saw this as an opportunity and a threat? Humans as an uplifted race were already considered a wild card and Shepard has proven to embody that and more. What if the Reapers saw Shepard as a fulcrum, have her unite the galaxy, deliver the best and strongest to Earth while slowly breaking her overtime. Once she becomes fully indoctrinated and breaks, the rest will follow. They'll follow her to the depths of hell. Liara kept saying in ME3 that she doesn't know how she does it, how she keeps fighting, how she keeps everything together. Shepard even *SPOILER* influences Aria T'Lok to have a change of heart. If you overlay a veil of indoctrination over all of the impossible things Shepard accomplished, it makes more sense than a Disney-esque we all gotta work together friendship is the best explanation. That leads to ME3 and the hallucinations, dreams, and finally the events on the Citadel. Finally have her broken. The Crucible didn't fire, Anderson is dead in a very emotional scene ( I loved it when he called her "child". It was so sweet. And if it was in her head, it's all the more sad as he really was a father figure to her), there is no hope. There something else that was pointed out in an AngryJoe video ( I've only watched his ME vids): Shepard's eyes. In the Synthesis and Control endings, right before Shepard falls away, her eyes look like TIM's. Destroy does not. So, let's say that Shepard WAS on the Citadel, hallucinating, found the control panel that ignites the Crucible or whatever, Reapers make one last push to indoctrinate, Shepard breaks free and by that the strongest psychic link is severed and Shepard either falls back to Earth or wakes up on Earth. And what about re-entry if she was in space? She got spaced before. Her body was recoverable when she died in ME2, it wasn't just a pile of ash and goo. The deus ex machina here could be the armor/ biotic technology. That's a good suit. I don't know. I'm still new to this relatively speaking
Anyway, enough of my ramblings. Thank you again. I can't bloody wait for ME: Andromeda.