When reaching the acceptance stage it must be done at your own pace and must be dealt with in your own mind. I think I've finally reached that point. I've been investigating the Indoctrination Theory via posts, youtube videos and blogs. To be honest, I don't buy it, not in the way it is presented. The way the IT is typically presented it that after Harbinger blasts the ground in front of her, Shepard is knocked back and from then on everything happens in Shepard's mind. She is battling indoctrination and if she picks either control or synthesis, Shepard loses the battle. If she picks destroy, Shepard resists indoctrination and (if EMS is high enough) Shepard can live to fight another day. Unfortunately, the only way this works is if the game isn't finished and the "real" ending is coming via DLC later on. The theory on that is that the original story got leaked and BW didn't have time to completely do a new ending, so they made a temp ending to give them the time to finish it properly.
I don't buy it. 95% of everything proposed by the IT (Indoctrination Theory) can be explained away by ME3 being a rushed product, game play mechanics changing to further the story, inept writing, "speculation from everyone" and simple coincidence. However that does leave some other oddities, mostly Shepard clinging to her left side starring at a gaping wound in the same place Anderson had just been shot. Digging into PC files, players have found the foliage on the planet the Normandy crashed called "Dream_Foliage." That's a pretty big indication that the entire Normandy crash was a dream or in Shepard's mind. Still, I don't fully buy IT as it is presented. For me it is entirely possible that the events of the final are happening in Shep's mind AND in reality at the same time. In other words, IT could be probable, but the ending we got is still the final ending. If the game isn't finished, then why would BW bother w/ the EC?
Anyway, just my opinion and I'm sticking to it, though I think destroy is still the best ending. ;P
If you want to learn everything you can about the IT, go to INDOCTRINATION: The Definitive Guide to the Mass Effect 3 Ending Co... If anything, it is entertaining.
EDIT: For those interested in the IT, the author who compiled the above information has a new site that delves even further into the theory.