The Indoctrination Theory is one of the most popular alternative readings of Mass Effect 3's ending scenario. It supposes that Shepard, by the time he reaches the Crucible at the end of the game, has already been indoctrinated by the Reapers after being slowly manipulated over the course of the entire trilogy.

According to this theory, the events at the end of Mass Effect 3 aren't even literal - they all play out in Shepard's head. Fans have put together pretty strong cases for backing the Indoctrination Theory up over the years. However, it's never really been clear as to whether the evidence was put there on purpose, or if fans managed to connect dots that were never intentionally placed in order. We recently learned that it is very much the latter case.

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During a conversation about an alternate Mass Effect ending that didn't quite make the cut, Mass Effect 3 writer Chris Hepler explained that he's a big fan of the Indoctrination Theory. However, he was also clear about the fact that Shepard being indoctrinated was never on the cards at BioWare - it's a theory that was completely born from fans.

“The Indoctrination Theory is a really interesting theory, but it's entirely created by the fans,” Hepler explains. “While we made some of the ending a little trippy because Shepard is a breath away from dying and it's entirely possible there's some subconscious power to the kid's words, we never had the sort of meetings you'd need to have to properly seed it through the game.

“We weren't that smart. By all means, make mods and write fanfic about it, and enjoy whatever floats your boat, because it's a cool way to interpret the game. But it wasn't our intention. We didn't write that.”

So, if you subscribe to the Indoctrination Theory, you can rest easy knowing that Mass Effect writers think it's a perfectly reasonable way of interpreting the game. However, it wasn't what the team had in mind during development, meaning that the Destroy/Control/Synthesis trifecta is still technically canon.

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