Or they could make indoctrination theory the canon ending... which would be the best thing ever.
So rather than kill all the Reapers, you would go with Shepard is brainwashed and the galaxy is screwed?
That WOULD be hard to explain. Yeah I have no idea how they are going to do it.
Honestly its one of those fan theories about how things should have gone which totally ignores what the last 2 games had previously said on the subject.
As this one seems to totally ignore how indoctrination actually works.
Much like how people were clamoring for an option to fight the Reapers conventionally despite Mass Effect and Mass Effect 2 pretty much explaining it was suicide as the Reapers totally outmatch everyone.