Not only did the Reapers of Mass Effect 3 fool a lot of people into doing their bidding, but they also fooled a lot of them into thinking that its ending was terrible and made absolutely no sense.
First and foremost, it has become very clear that Shepard is being indoctrinated by the Reapers since the beginning of the third game. This image (http://i.imgur.com/DkXPT.jpg) highlights the key symptoms of Reaper indoctrination from the codex itself. This image is crucial to understanding the final moments of the game, as what happens during them fits entirely within those symptoms.
The main thing I took away from that ending is the fact that the so called “Catalyst” during the last thirty minutes of the game is nothing more than a lying Reaper. Everything it says makes no sense whatsoever. What reason is there to believe that Shepard can control the Reapers after you just watched someone try and fail? Why would there be no more war if everyone was merged between synthetic and organic? The Geth were a completely homogeneous society in being and thought, and even they fought amongst themselves. And let’s not forget that this “neutral option, of merging synthetics and organics, is what the Reapers have wanted all along. This has been their “solution” to the “chaos” from the very beginning, despite the fact that you reaching the Catalyst proves his “solution” wrong (as admitted by him when you arrive).
The Catalyst is a Reaper taking the form of the child killed in the beginning of the game in order to co-opt a sense of trust and familiarity with you in a last ditch effort to save itself. It’s why destroying the Reapers is suddenly the Renegade option with Anderson himself being painted as a Renegade as well. The Catalyst is doing everything it can to dissuade you from killing it. Again, the symptoms:
“The Reaper’s resulting control over the limbic system leaves the victim highly susceptible to its suggestions…A Reaper’s ‘suggestions’ can manipulate victims into betraying friends, trusting enemies, or viewing the Reaper itself with superstitious awe.”
That second bit is the ending word for word. Throughout the entire game you are having visions and whispers in the back of your head as you chase after this image that is now used to deceive you, which itself is a symptom of Reaper indoctrination. People around you are becoming paranoid in the Citadel, and even your own crewmates are beginning to follow suit. In addition to all of this, there is simply no reason to believe anything the Catalyst is saying. There will be no peace if the Reapers are destroyed? The entire game is spent uniting the galaxy for the first time in its history. We have Geth living with Quarians and Turians fighting next to Krogan. We have overcome every sour note of our existence to defy the Reapers, yet there will be nothing but war without them? Just like the organics must be saved from the synthetics by killing the organics?
People are taking these proclamations at face value and believing what the Catalyst says without ever pondering the possibility that maybe this thing is lying on purpose – they, going by these symptoms, are as indoctrinated as Shepard is. The endings don’t make sense and there are “plot holes” (if we really want to call them that) strewn about because it is all one big, giant, elaborate lie. Anderson suddenly being a Renegade doesn’t make sense because it is a lie. The ending was a giant “Fuck You” from Bioware to every single person who ever mashed the Paragon or Renegade option without ever taking a second to think about what they were doing at all – simply swap the colors around and suddenly nobody knows what to do. You can even fool them into completely abandoning their mission (which was to destroy the Reapers) and to save the very people they’ve been set against for the entire trilogy.
For the final moments of Mass Effect 3, you are talking to a Reaper. It is literally doing everything it can to fool you into thinking it's your friend, and that by destroying it, you will be destroying yourself. It even warns you that if you decide to kill the Reapers, you will kill all synthetic life including yourself (given that synthetics are the only thing keeping you alive). Yet why is it that if you do choose to destroy them, it is the only ending of which you can be found alive and still breathing? Hell, what even is a catalyst?
It's a harbinger. They're synonyms. A catalyst and a harbinger are the same exact thing. The Catalyst is Harbinger, viewed by Shepard with "superstitious awe." You've been talking to Harbinger this entire time.
Nobody is taking the time to read between the lines. Bioware pulled a fast one knowing that there would be a lot of people willing to listen to a Reaper if they managed to do it just the right way, and everyone is getting too mad to even realize it. The whole ending was a clever ruse that deserves way more praise than it's getting right now.