Some are saying that the Catalyst is actually Harbinger communicating with Shep. It was odd that it was Harbinger that attacked Shep + team when they were running towards the beam. What's the significance of that? Why Harbinger and not any other reaper? And then it just gets up and flys away after firing a few lasers? I don't think so..
I thought it was odd as well. I have a theory to it, though. The indoctrination is to get Shepard to make the wrong choice at the end. When you wake up, you see no squad mates or anything nearby. One guy on the ground is reaching out to you, not the beam, and dies when you reach him. Harbinger flies off, possibly trying to leave the impression of a false sense of security for Shepard for the husks and marauder to take him. Since you're armed, that part of the indoctrination fails.
So you then make it to the beam, supposedly. Now, here's where things really start getting weird. You land inside the Citadel, but it's a section you've never seen or been to. The moment you get up, Anderson is suddenly greeting you on the comm and asks if it's you, not if anybody is alive. Also, right before this, you hear faint and fuzzy radio chatter of marines talking about how nobody made it in the beam. How would they know this? Unless, you really haven't got up to head to it and are still laying in the rubble. Those faint voices are just barely there, possibly from reality just barely slipping through.
Anderson states he came in the beam after you had gone in. Then he states he's a different part than you but has the same look. When you open the door to see the guide towards the room ahead, there's only one way in. You would have seen him go in there. Next, where did the Illusive Man come from? This part seems to be more along the lines of Shepard's conscious fighting and arguing, trying to persuade him into thinking letting the Reapers live is a good idea. You can also see the Illusive Man trying to force the influence by the black strands around the screen. Possibly Harbinger trying to bear down on the indoctrination to cripple your views.
This part was really neat, to me. Usually, choosing paragon results in trying to talk your way out as peaceful as possible. Here, Shepard doesn't try talking out of it. Instead, it seems more like the renegade option by egging him on. You're constantly harassing him about the Reapers controlling him and telling him if he can control them, then do it. Then it seems like a throw-back to Saren. The Illusive Man, like Saren, was indoctrinated and sees now that it's far too late to turn back. The both take the only way out they can see fit after harassing them: Kill themselves.
Choosing other options seems to result in shooting the Illusive Man yourself. Much more like a proper sense of things, taking care of the situation on your own. Shortly after, Anderson dies and seems to be another attempt of Harbinger tearing down those mental barriers of Shepard. Weaken Shepard more. Hackett comes up on the comm and tells you that you need to do something to active the Crucible. Shepard then gets transported to another random area in the Citadel.
You're greeted with a being that says it controls the Reapers. Yet, all Reapers are sentient. This part makes me think that, possibly, Harbinger is trying to make the Reapers look less harmful and more like just pets that can simply be controlled. The don't think or act without guidance. This is what the Illusive Man tried to teach you. The being then states that they cannot choose any of the 3 options laid out before you. That's odd. Very odd, considering they already stated they control the Reapers, yet one option is to control the Reapers as well.
The being also states that if you choose anything but destroying all synthetic life, you will die. He makes it very clear in tell you, as well. Shepard even second-guesses the proposition of destroying the Reapers with, "Maybe," since it's not clear if you'll die or not. Being absorbed will obviously kill you and make you, as well as everyone else, corruptible via Reaper code now. You saw first hand what happened to the Illusive Man for trying to control the Reapers. Thing is, the new DNA strand of synthetics and organics as one is supposed to look most appealing because this is what the Reapers want.
Choosing to destroy the Reapers, and possibly all synthetic life (maybe even yourself, seeing as you're part synthetic), seems like the right way to go. After all, you came here for one purpose, not two other ones. Destroying the Reapers seems most appropriate. After Reapers are destroyed and the Citadel and Catalyst are gone, you're shown some rubble. Shepard's body lays motionless before a swift intake of air. I believe that intake of air was Shepard returning to reality after the attempted indoctrination. Destroying the Reapers broke the hold Harbinger had on him and now Shepard's back, alive, laying in the rubble from the blast near the beam.
There are a lot of other little details, but this is just the basics of it. Don't jump to conclusions, either. After all, this is just a theory and could easily be swept away. As for what happens AFTER waking back up? I don't know, we aren't given that. DLC, possibly. Anyway, enjoy the read and I hope it may help some of you see the ending in a different light.