Ok, so I'm building off the indoctrination theory being at least partially true. Shepard wakes up, seriously wounded, after Harbinger's airstrike (He/she's managed to survive because 1: Harbinger wasn't using his main gun, which would have destroyed the Conduit as well which Harbinger needs to process all his new thralls with. The blasts came from smaller auxiliary lasers instead and 2: Shepard was only on the edge of the blast, it didn't hit him directly).
You survive whatever choice you made. However, what you chose dictates how much latent indoctrination is still present and how it presents itself, with hallucinations and voices in your head reflecting whether you chose Destroy, Control, or Synthesis.
Shepard, unable to move quickly or defend himself, then has to stealth his way to the conduit without being spotted by Reaper patrols and Husks. Your latent indoctrination will try to lead you astray and into the path of danger, so you need to be observant as to what's real in the world and what's trying to trick you.
If you reach the Conduit it teleports you right to the top of the Citadel tower, where you open the station's arms and let the Crucible in. This is when you discover the the Crucible is basically a giant supercomputer, the only thing in the Galaxy with enough processing power to hack into the Reaper mainframe itself, allowing you to literally get inside their 'mind' where they are most vulnerable. All it needs is someone to operate it, that someone being you.
So through the Crucible you upload your consciousness into the Reaper mainframe (this will play out very much like that mission with Legion on Rannoch, as well as ME2: Project Overlord). You fight your way though to the very depths of their collective consciousness, while they try and block/terminate you through various means. The final fight will be with Harbinger's 'avatar' inside the mainframe (exactly how this fight would play out I'm still thinking about). Once you've killed Harbinger, the loss of his consciousness from the mainframe momentarily 'stuns' the Reapers, essentially putting them on standby as they try and reach concensus on who their new leader will be.
This is where you get the choice between Destroy and Control. If you choose Destroy, the Reaper threat is wiped out for good. However, the consequence will be that Shepard dies, as his consciousness is deleted from the main frame along with the Reapers, and his body is left brain-dead. If you choose control, Shepard survives and the Reapers can also be commanded to help the Galaxy rebuild. However, Shepard is aware of the latent indoctrination, and can express through dialogue that trying to control the Reapers is a big risk, and may have unforeseen consequences in the future. It's up to you to decide whether your Shepard's survival makes that a risk you're willing to take.
In the ending cut scene the Reapers either keel over or declare their allegiance to Shepard depending on what you chose. Your overall Galactic readiness, as well as you rep with your crew mates, determines who survived and who died back on Earth. It will be possible to save all the major characters, but only if you've done pretty much everything (I wouldn't want to make it too easy on you
) If your Shepard survives, you see them awake back in reality, get picked up by The Normandy (or Admiral Hackett if the Normandy gets destroyed, I'm going to make that an option) and rejoin the survivors. If you die, then it cuts to your funeral, held on Earth, with all the survivors present.
Roll credits
