Alright guys, say it truly is the indoctrination theory.
After Shepard starts breathing after the Destroy ending, how would YOU end it?
My problem is that if Shepard is indoctrinated, you don't have a character to play as anymore. It would feel extremely awkward to switch characters outside of a sequel or expansion, so DLC doesn't really cut it for continuing the story.
If he beats indoctrination, he is a beat up corpse in need of severe hospitalization and the Reapers are still busy kicking everyone's ass. The best thing here would be to have one of the two crew members you took with on the final assault make it to the Crucible and succeed, but we'd still need some sort of definition on what the Crucible/Catalyst actually is and what it does.
Easy route is it wipes out all Reaper tech, but then what is the conflict that the DLC needs to answer? Are we dealing with some internal conflict as all the stranded races in the Sol system try to figure their shit out? There is no obvious bad guy anymore unless one of the friendly races turns or magically a Reaper or two survives. Its going to feel really forced depending on the outcome of the Crucible/Catalyst.
And if the Crucible/Catalyst plan fails, its going to require some universe punching power for the allied species to win this.