Can someone please explain the Indoctrination Theory for Mass Effect 3?

first off, i made the mistake of playing Mass Effect 3 before Mass Effect 1 or Mass Effect 2 so i do not have any leverage from previous games to back me up. Secondly, what i do know of the indoctrination theory seems blurry to me. i know that apparently the reapers were trying to control Shepard throughout the whole game (possibly the whole series?) and that the everything after you running to the white beam to get the citadel is all fake and the the three ending choices are related to his indoctrination, which to me does not make any sense. also, i chose to destroy the reapers and at the very end they show shepard and he wakes up and take a breath. i was reading in a forum of someone's take on this indoctrination and he said that when Shepard woke up, the reapers were not destroyed which meant that he was under full control by the reapers and the war was still raging on. BUT HOW DOES ANY OF THIS MAKE SENSE?? if you could please give me a detailed explanation of all this it would be much appreciated. thanks. and how and/or could this lead to further DLCs in the future, considering that there will not be a sequel to Mass Effect 3, which really sucks because im starting to like this trilogy.
 
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