So let's say that the Indoctrination Theory is true (or retconned into existence by Bioware). What then? DLC obviously. But how should that DLC play out? Should it be implemented as a separate mission that shows up on the galaxy map after you've beaten the game? Or should it simply be an extension of the endgame? I think the latter option, if possible, is the best approach. So what should happen?
I guess the obvious beginning is for Shepard to wake up near the Conduit. Maybe alter the "Lost" planet ending so that the LI turns to the camera and says "Shepard! Wake up!" Then BOOM Shepard is awake, there are Reaper forces everywhere, Harbinger is still firing. Suddenly Shepard is being pulled to his/her feet by the LI.
We hear Harbinger mocking Shepard. It's giant laser targets Shepard and his squad. There's nothing Shepard can do. He just fires at the Reaper forces around him, trying to hold them off to allow someone, anyone, to get to the conduit. Harbinger fires....the Normandy swoops down out of nowhere to deflect the blast and take on Harbinger. Joker isn't going anywhere. He's in this until the end. The Normandy manages to disorientate Harbinger then cuts a path through the Reaper forces to the Conduit so Shepard and co can continue on. They rush to the Conduit and are transported to the Citadel.
We then take a page out of KOTOR's endgame. Shepard and his squad have to fight their way through seemingly endless Reaper forces on the Citadel as they try to get to the Catalyst. As they fight, Harbinger is in Shepard's head. Taunting him about the indoctrination. If Shepard chose to destroy the Reapers, Harbinger talks of his willingness to destroy galactic civilization in order to save it, much like a Reaper. If he chose synthesize, Harbinger talks about Shepard's willingness to become what he has tried to destroy. If he chose Control, Harbinger accuses Shepard of being just like Illusive Man. As Harbinger taunts him, Shepard continues fighting towards the Catalyst. What happens when he gets there? Download the non-existent DLC to find out. Ha.