The Indoctrination Theory cannot work. In fact, it would cause a plot hole because Vendetta would not talk to you on Thessia if you were indoctrinated. Also it would completely wreck the rivalry between Shepard and TIM.
The ending simply put, does fit the franchise. The entire series was about how actions or decisions of one (or a group, race, person, whatever) can alter and affect the destinies of others and how this leads to conflict and bad consequences, especially if ignorant or unaware of the consequences the decision has on others. Think of it like this. How many quests in the series dealt with an AI project gone wrong? Or an attempt to control lifeforms to be used as tools that backfire and kill the lab? Or a race that was uplifted to solve a problem that led to problems and conflict later on? All throughout the series. Well, the Catalyst, the starchild, starbrat, whatever not only fits this theme, but twice over, as a way for its creators to control its subjects and then it controls the destinies of advanced civilizations in the galaxy after it backfires against its creators. Its a sci fi ending, hell, it puts the Mass Effect in Mass Effect. This is NOT Guardians of the Galaxy as a lot of the idiot fanbase thought it was.
And the Extended Cut, showed you the consquences of your actions, not just the final choice. hell, I got the outcome where the Rachni settled the Krogan homeworld in an ironic twist.
It amazes me that you still to this day can't handle people having a different opinion than you.
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