i finished the game yesterday along with EC DLC and i think the Indoctrination Theory speculated on the net everywhere could be correct. I'm a big fan of ME honestly and is now pretty much pissed off on the ending... i mean he/she's Shepard! I would like point out few things maybe i'm incorrect but still i would like to say something about them..
First when destroyed the Reaper with the last rockets and went near the beam and saw another Reaper came and everyone was marching towards the Beam and one of our squad member (whoever he/she was based on players choice) got pretty much beat up and was bleeding all over.. in my case it was James and Garrus and James was bleeding and could'nt even walked properly and Shepard then call Jeff for his squad evac! now shepard running and the Reaper Red beam suddenly destroys our path and threw us right? screen turned white and you found your self alive and your armor is gone probably break into pieces and Shepard is bleeding badly and barely even walk now we try to walk towards the light and shoot a couple of husks! You go up found hundreds of bodies lying around you and you talk to anderson.. lets not go into more details.. Chances are when the Reaper shot the Red beam which tried to kill us and screen got white like getting in unconcious state here's the Indoctrination or Illusion starts.
Secondly as you already know that throughout all 3 parts our choices are based on Paragon (Blue) and Renegade (Red) choices good/evil choices right... that God child gave us 3 options? So here we get Destroy ending in Red, Control ending in Blue and Synthesis ending in Green.. The Illusive Man wanted to Control the Reapers! Seren wanted Synthesis i guess (if im not wrong) and Shepard, Alliance and everybody in the Galaxy wanted to Destroy the Reapers once and for all! now if Destroying is the better ending as compared to the other 2 so why it has Renegade color (Red)? and controlling that's like power hungry and worst ending according to the majority of fans has Paragon color (Blue) and last but not least Synthesis which is the Final Evolution according to the Godchild! So hope you understand what i'm trying to say here.
3rd.. all 3 major endings (talking about with high EMS not to mention other worst endings) are quiet same and if you have Full EMS or in easy words Full Green Bar for Military Strength you will see the Crew crash landed or landed intentionally or idk what happened on a beautiful Island and everybody seems to be Physically fine! i mean if you remember one our squad mate got pretty banged up some hours ago hmmm... no bruises no bleeding. If you choose Destroy (Red) no scene of EDI appear that what happened to her and Jeff is standing there who is very attached to her or it.
4th point is when you choose Destroy ending you see in the End Shepard takes a breath in the rubble looks like rocks and idk but Citadel did'nt had any rocks around and than there were N7 tags. That seems more like a place when Reaper hit us on the ground with it's Red beam before running and going into the white beam that leads us to the Citadel.
Final point about Stargazer... He said it all happened very long ago and probably he's telling stories to his son or grandson and when the kid asked when i will go to the stars the old man said "one day my sweet" he did'nt said it's not possible or space traveling is finished.. coz nobody let their little kid go far alone at that age and suprisingly the Stargazer has another story about shepard to tell...
Shepard is'nt dead and none of that happened actually and whatever happened in the end was going inside Shepards head! The reapers tried to control his/her mind and made him believe that it's happening in real and showed him the paths they wanted.
Reaper Indoctornation wears off when the person is injured on witnessing a near-death scenario, take it from Matriach Benezia in Mass Effect 1. She said herself that Indoctornation was weakening when we shot her. So no, What you saw was real, no hallucination or indoctrination there.
As far as endings go, Destroy is a bad ending. Killing off EDI and the entire Geth race, you call that paragon? Whereas controlling them gives you the chance to save everyone there is without any further collateral losses.
The crash scene can be set several hours or even days after the reaper purge took place. And if you're taking about the Normandy, well that ship handled a badass crash on collectors base and the crew remained alive thanks to its new kinectic barriers and shielding. What to say that it couldn't survive that crash with all of its crew still breathing.
But yes i do agree that the last breathing scene is still to be covered but there's no indoctrination taking place, its just a random idea came up by random guy to weigh down the Mass Effect 3 ending controversy. The Leviathans revealed all about the Catalyst, their own fault which started this cycle.
also im not calling Red ending good if you read the post clearly 
