Being the real ending or not, indoctrination theory is somewhat one thousand times more interesting than any other ending in Mass Effect 3. Did Bioware ever belie this theory? I'd love this theory to be real because it would mean the fight against the reapers would not be over and we would end it in Mass Effect 4 whith a new character.
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The extended ending invalidates the indoctrination theory.
The indoctrination theory relies on the fact that what is happening after Shepard reaches the beam isn't real and is taking place inside Shepard's mind. The extended cut refutes this by clearly saying that Shepherd did indeed reach the citadel, meet with Anderson, The Illusive Man and the Catalyst and therefore the indoctrination theory cannot be true, no matter how much more interesting it would have been.