Please don't read if you haven't completed Mass Effect 3. This thread will have spoliers.
Let's just pretend the indoctrination theory is correct.
What if Shepard is indoctrinated in Mass Effect 4 and he plays as the primary antagonist of the game. Though this isn't very likely it would be an interesting turn in events.
Here is how I would make it work. You can only import your game into ME4 if you have enough gallactic readiness to fight back the Reapers and you chose the destroy ending, fighting off indoctrination. In the DLC Shepard would have woke up, unfortunately upon awakening the citidel has been destroyed by the Reapers. Making it difficult to easily destroy all of the Reapers. The fleets of the galaxy Shepard has amassed is large enough to fight back the reapers and send them into hiding to plan another attack.
Leading into ME4 you play as a new character that is being trained by Shepard to become a new human Spectre. Unbenonced to anyone that Shepard, though previously fighting off indoctrination, has become indoctrinated. (As stated at several points in the series that even the strong willed can only fight indoctrination off for so long. Once indoctrinated, it is perminant and a Reaper does not need to be present.) Eventually there would be a showdown with your new character trying to take down Shepard.
What other ways do you think that Shepard could be worked in as the antagonist of ME4?
This is just for fun, I highly doubt Shepard will be more than a few data pad entrys in ME4.
