ballin4life
Smash Hero
presumably the brilliant writers at bioware who wrote things like the Rannoch plotline and the Tuchanka plotline (which have tons of resolutions that vary greatly depending on your choices, both prior to and during the mission) could come up with something.If the IT theory was real this is what would happen:
The game would end without a resolution. Or, there would a whole section afterwards that you would only get if you had a high EMS and picked destroy, which would make that element of choice pointless as the other 2 endings aren't real. Upon getting it everything would play out near identical, Shepard would still be injured, TIM would have to be resolved and so would the Crucible. Now what to do with TIM? Make the 2nd biggest antagonist in the series get a quick anti-climactic end, or give him yet another 10 minute long scene.
Whatever the case you would basically be playing out everything you already did a few minutes ago, and then you'd end up at the Crucible. What does it do this time? Well most people seem to stumble when asked this, but the general wants are it to be a massive laser, which I assume means every Reaper would have to get in single file directly infront of it, or some sort of pulse that disables the Reapers weapons, shields and indoctrination tech. In otherwords a slow version of the destroy ending.
So if it were real you'd either have to leave everything unresolved or get a high EMS and pick destroy, replay everything again with slight differences, then pick destroy again. That's not a better ending, if people complained about their choices not mattering then they'll complain even louder once they realise they're getting railroaded into choosing one ending.
see, in those, there is in some sense only one ending - somehow the conflict is resolved and shepard gains the allegiance of a group. what gives the sense of multiple endings is HOW that conflict gets resolved. you could have the ending be "destroy the reapers" but have it play out many different ways depending on your choices throughout the game. you shouldn't get your multiple endings by shoehorning in random choices at the end and having that choice be the only thing that matters.
regardless, if you wanted to do an "indoctrination theory" ending you could have shepard wake up from being indoctrinated (with some bonus if you resisted the Reapers by picking destroy in the hallucination), fight a boss fight against the Illusive Man who is being controlled by Harbinger (similar to the Saren/Sovereign boss fight) and then have a final confrontation with Harbinger that answers all the questions about where the Reapers came from and what all. Then have Shepard activate the Crucible, but make it so that it takes like 2 hours to charge up or something, so then all your fleets have to defend it for a bit and then based on EMS it can fail/work partially/work totally/whatever. hell, you could even have one more mission on the crucible/citadel itself (say the Reapers have to board it to blow it up from the inside maybe). either way, montage of your war assets fighting, then the crucible finally fires and GG Reapers.
that's a really basic template off the top of my head. it's obviously possible to write a coherent indoctrination theory ending.
anyway the main point really should be that the "assume that all really happened" ending is worse than the "no resolution bro it was all just a dream" ending and that's saying something