canon ending of Mass Effect 3, even though many players found this part of the trilogy to be lackluster. Alternatively, there's a way to continue the story of the original trilogy without having to pick one of the endings.

Mass Effect 3 has three primary endings and one extra ending, and each of them would create a completely different set-up for ME5. The Destroy ending tends to be considered more likely to be canon compared to the others, especially with the extra scene that shows Shepard taking a breath in the rubble if the player has enough War Assets. Then, the Synthesis ending combines natural and synthetic life, while the Control ending has Shepard take control of the Reapers. Finally, choosing not to pick an ending results in Shepard watching the Reapers destroy ships from the Crucible.

What Is The Indoctrination Theory?

Mass Effect's Contested Fan Theory

The short answer is that the Indoctrination Theory is the idea that Shepard is in the process of being indoctrinated by the Reapers to their side, and that the ending sequence is where the indoctrination culminates to the point of either being successful, or Shepard manages to overcome the Reapers' influence. Players created the Indoctrination Theory as an ending that feels more fitting for the series, and make sense of the multiple plot holes and strange moments that don't feel like they fit into the story. A lot of details make the theory seem intended to an extent.

The Indoctrination Theory has been repeatedly confirmed as not what the developers intended, but it does fit into the last game as a way to explain the parts that felt like they didn't quite belong. This leads players who subscribe to the theory to believe that it may have been part of the original story, then changed at some point during development, which resulted in pieces of it being left in the final version of the game. It doesn't help that what Shepard experiences fits with descriptions of indoctrination as told by in-game characters.

Since indoctrination has been part of the trilogy from the first game, and the Crucible was added in Mass Effect 3 without being mentioned at any point before that, the Indoctrination Theory isn't an idea that came from nowhere. Saren, the first main antagonist, is revealed to be indoctrinated, and The Illusive Man in Mass Effect 2 is likely in the process of being indoctrinated, or has already succumbed to the Reapers' influence. So, it's already been a theme that Shepard has encountered multiple times during their journey.

Signs Shepard Could Be Indoctrinated

How This Theory Fills Plot Holes

In general, indoctrination isn't well understood by the races in the Milky Way, which makes sense considering that they were unaware the Reapers existed at all until it was time for another cycle of harvesting to begin. However, various characters who have been subjected to indoctrination or witnessed others affected by it have put together common signs. The residents on Eden Prime reported that they heard a horrible noise when Sovereign descended. Rana on Virmire describes it as a subtle whisper that makes somebody obey without question, which gradually turns those affected into mindless slaves.

The Rachni Queen showed some resistance to indoctrination, but the Rachni around her succumbed to the Reapers' songs, and she described them as being filled with oily shadow figures. Other characters, such as Saren, try to keep control of their minds by proving themselves invaluable, but Shepard accuses Saren of being fully indoctrinated without realizing it. All together, it looks like indoctrination wears away at the target's mind, making them hear sounds, whispers, see hallucinations, and believe that they are still in control of themselves, at least from what characters who have experienced indoctrination say.

Having been exposed to a lot of Reaper technology, it's surprising that Shepard doesn't show many signs of indoctrination until Mass Effect 3. However, there are multiple moments from the beginning of ME3 that build a case for the Indoctrination Theory. First is the boy that Shepard sees during the escape from Earth sequence, which many players believe is a hallucination, but one that could be due to the psychological stress of the situation. However, the boy reappears multiple times as a dream or image, and he always speaks for the Reapers, which seems like part of indoctrinating Shepard.

Additionally, Shepard has multiple dreams that fit the Rachni Queen's description of oily shadow figures. If the dreams are due to trauma or stress, there's no need to fill them with oily shadow figures for them to be effective. However, the biggest argument for the theory is in the final sequence, where The Illusive Man is at the Crucible's controls for an unexplained reason, and Anderson somehow beat Shepard to the location. Finally, the last choices flip the morality colors. Control – the worst and most reckless option – has the Paragon color (blue), while Destroy is the safest option, but it's Renegade's color (red).

How The Indoctrination Theory Could Set Up Mass Effect 5

Creating An Unexpected Journey

There are actually a few benefits that come from using the Indoctrination Theory as the canon ending of ME3. First, it avoids making one of the three main endings canon, but it comes with the perks of the Destroy ending while allowing the use of Mass Relays in Mass Effect 5. Instead, it could be explained as the Milky Way coming together with enough strength to defeat the Reapers, even if that took years to accomplish. It also raises the question of what happened to Shepard and where they might be, considering they were on the verge of being indoctrinated.

The Indoctrination Theory has been debated a lot in the Mass Effect community, and it seems to be either loved or hated. Even if it doesn't seem believable, it's tough to deny that the theory doesn't fill in some of the many plot holes in ME3. Because of this, it would be unexpected to see it become canon, but it comes with some storytelling benefits that the developers could capitalize on in Mass Effect 5.