Ahem
First off I'd roll with the indoctrination theory. So you'd have the 2 "endings" and the one continuation where your Shepard wakes up among the rubble. Now depending on your EMS/choices/Paragon and Renegade; Anderson could either be dead under the rubble, dying or alive with injuries. Reinforcements show up IF you cured the genophage.
As the reinforcements push for the beam, Harbinger focus' it's attacks. Here's where your choice to resolve the Quarian/Geth conflict comes into play. If you did, there will be enough ships to cover the fight above Earth so the Normandy flies in to help against Harbinger. If you have high Paragon or Renegade/EMS/upgraded your ship from ME 2 then the Normandy will survive and push Harbinger away. If one of those requirements hasn't been met the Normandy is either damaged or destroyed. If Damaged or Destroyed, Shepard never makes it to the beam, either to help hold off incoming Reaper forces or be killed by Harbinger. In that scenario an unnamed solider makes it to the beam but it ends on a cliff hanger.
Assuming the Normandy survived, Shepard makes it to the beam but the transportation fries his weapons. Upon entering the Citadel, they sees the bodies of C-Sec officers and Cerberus operatives. Scrapping some left over armor and weapons, they either discovers Bailey's body or finds him holding his position in a security office; revealing that all the civilians were able to get off the Citadel in time(once again depending on your choices and personality) if not; civilian bodies will be laying throughout the Citadel. If Bailey is alive then the race to the crucible console is a bit easier, if not get ready for a long drawn out trek.
Along the way, Harbinger; still in Shepards mind, tries to persuade them. Creating images of the squad mates dying, being harvested and convincing them to join the Reapers. Either Shepard gives in or they fight off the attempt. As Shepard nears the console, a keeper approaches them; revealing a Prothean AI stored in the keepers as part of the Protheans reprogramming. It allows Shepard to touch Harbingers mind where they learn of "dark energy". After this, the AI wipes the traces of Harbinger from Shepard but by doing that it terminates itself.
Now free from any more indoctrination attempts, Shepard pushes to the final room. The crucible terminal; where the Illusive Man is waiting. Looking normal, he attempts to convince Shepard to work with the Reapers and allow them to process Humanity and turn them into the next Reapers; giving them galactic superiority. Shepard can either agree or talk him down. Talking down leads to a shoot out. If Bailey is alive, he'll activate nearby automated turrets to help. If not, hope you brought a lot of medi-gel.
Either you agreed or talked down, Shepard and the Illusive Man will come face to face in front of the Catalyst console. A giant interface that sends out a signal. You can either talk down the Illusive Man and convince him to face his errors (he doesn't shoot himself in the face if you are high Paragon), kill him, allow him to merge humanity with the Reapers, high renegade he commits suicide or fight him. Which would be difficult as he has Reaper level biotics. Either way, when Shepard reaches the console they are greeted by an image of Harbinger masquerading as the Shepard opposite of your own. So if paragon Shepard, Harbinger will appear as Renegade Shepard and vice versa. If Illusive Man was left alive, he'll keel over in pain as this is another indoctrination attempt.
Thanks to the Reaper signal purge by the AI, Shepard can resist it and confront Harbinger. With the Normandy hitting Harbinger hard, it becomes desperate and commands Shepard to not activate the catalyst. Shepard can either comply or put the pressure on Harbinger by bringing up Dark Energy. That the reapers were once organics, afraid of their own mortality so they sought to live forever. With the discovery of Dark Energy, the Reapers feared that organics left unchecked will discover a way to end their 'perfect' existence. The Crucible sends out a signal that disrupts dark energy. Not only severely disabling the Reapers but possibly shutting down the relays by disrupting their own dark energy by sending the signal through them. If high paragon, Shepard will warn the fleet of what's about to happen, if high renegade Shepard will only warn the Normandy. You can choose to not warn anyone.
Either way, Shepard makes their choice and Harbinger phases out; damning Shepard. Now, if you kept the Illusive Man alive; he'll disable Shepard and activate the Crucible himself, dying in the process: Stating that he wanted to one up the Reapers and Shepard to prove his superiority. If not Shepard will activate the Crucible and either be severely crippled or die. The signal is sent out and the Reapers are made helpless as the ships blow them to hell. The signal is sent through the mass relays, if Shepard sent out a warning either himself or through the Normandy; the fleets head through the relays to get to their home planets before Shepard activates the signal. If not, they become stranded in the milky way. Either way, the Normandy heads to the Citadel and Shepard is greeted by their LI and most used squad member. They can either receive medical attention for their crippling injuries, die in their LI's arms or be helped by their LI and squad mate and limp out towards the Normandy. Then the credits roll.
If the warning was sent out, there is an after credit scene where it pans to the Mass Relay and just as it hints that the Relay is starting back up, the screen goes black. The End.
Things to note about how the ending can change. As Shepard, Hackett asks for advice on who should lead what teams where. These teams are scientific studies in reaper and Prothean Technologies. Keep in mind without these, the beam could fry Shepard and you get a shitty ending.
SWORD team. Which is the fleet, you need to manage who's in the front, middle and providing cover in the back. Same goes for HAMMER team (ground forces). This kind of micro manage will help ease the final push. It won't be a cakewalk but it'll make sure Shep needs to do what she/he needs to do.
Picking the right options will provide the least amount of casualties. Basically the suicide mission from 2 but on a grander scale. You can cock up and the Reapers win or push through and make your choices on the Citadel and receive the ending you desire.
No talk of synthetics vs organics. Seriously Casey, Asimov is spinning in his grave.
Phew. That took a bit but that's how I would have done the ending.
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