Mass Effect 3’s Extended Cut doesn’t fill all the plot holes, it allows you to peer deeper into them
Executive Producer Casey Hudson was correct when he said that the Extended Cut “is not a set of different endings, but rather it's an expansion of the original story. So we're trying to put on the screen what we imagined was implied by the original endings and address a lot of the feedback and the questions that we've received.” I'm sure Hudson and his team received a great number of questions during this conversation, and most of them seemed always quite reasonable to me. The original endings created this level of anger because they didn't make sense. Characters appeared out of nowhere, tautological arguments decided the fate of the galaxy, and physiological facts seemed to have been ditched in favor of high-stakes drama. Questions were raised and never answered. The Extended Cut DLC does fill many of the plot holes, and in that regard it is more satisfying. That being said, the holes are still there. This is disappointing, when a better option was created by the fans.
The Indoctrination Theory
The theory is far too complex and vast to explain here, but I'll attempt to (hastily) summarize: The Indoctrination Theory posits that everything that occurs post-blast from Harbinger takes place in Shepard's mind, and is not a literal version of what happened. Shepard's choice in the end is not whether to control, synthesize or destroy, but instead it is to accept or resist Reaper domination of her mind.The Indoctrination Theory could have turned the sub-par endings that shipped with the game into an impressive moment in storytelling. Not just video games, but storytelling. Why? Because we all bought it. We all believed, in the moment, that we were making real decisions. We might've had our suspicions about the Catalyst and the strangeness of the options presented, but few (if any) of us doubted them. Turning that sense of credulousness on its ear in the final moments of the game would have been an incredible achievement.
What we were given
But that's not what happened. Hudson and his team stuck, wrongfully I would argue, to their guns. They bought new, bigger guns. And when you couple Hudson's proclamation that there absolutely, positively, no way no how, never will be new endings with the content Extended Cut provides, it all but crushes the fan-constructed explanations. The endings are certainly stronger, but the Mass Effect team has only fortified a fox hole when a bunker was open for use just a couple yards away. The problems of logic and character persist, we were simply given more details about what happened after. The window was simply extended a little further to show the impact of your decisions. The power of video games as an art form is that not only can they match film and literature, but surpass them through interaction. Games can transport us and make us live the story instead of experiencing it from a distance. Shepard didn't make that final choice. Casey Hudson didn't. You did. Had the Indoctrination Theory been correct, it would have taken advantage of that power; you wouldn't have been interacting with the art, the art would have been interacting with you. The new content may be a letdown, but the Extended Cut is out, and I don't expect there to be more olive branches from BioWare in this area. It's time to begrudgingly accept the endings for what they are, and always have been: Imperfect and unsatisfying. Or maybe you liked the original endings. I won't condemn you for that. I'm also not going to agree with it.