A few thoughts on ME3 endings (inb4 "Not that crap again")
THIS CONTAINS SPOILERS FOR PRETTY MUCH ALL KINDS OF GAMES AS WELL AS A COUPLE OF BOOKS
First of all, I think that INDOCTRINATION THEORY (caps lock makes everything sound more intimidating) does make sense and has some interesting points, but I'm not going to get into that discussion as there are already enough people brainstorming it over and over again. Instead I am more concerned with what really happens while we're hallucinating in London and when (if) we come to our senses.
So yeah let's say it's all a lie, Shepard-Commander is high on stuff, Reapers are messing with his/her head, the Catalyst is not a random creepy god child and Harbinger is Jon Snow's mother (because every good theory needs that part). But then what is the Catalyst and what really awaits us past Marauder Shields? I've come up with a few theories:
Theory One: Bolvar is the Catalyst
Well, that's a pretty much obvious one. Once on top of the Citadel, you get a cutscene where the Catalyst encases Anderson in stasis, and then you fight it (it's easy, just don't stand in Indoctrinate and watch out for Harvesters trying to grab you) and eventually it insta-kills once it's health drops low enogh. Anderson then goes all deus ex human revolution machina and breaks free, and Illusive Man's ghost casts Project Lazarus on you (make sure to accept ressurretion). The three of you finish the boy off, and then there's another cutscene:
ILLUSIVE MAN'S GHOST: Without their master's command, the restless Reapers will become an even greater threat to this galaxy. Control must be maintained. There must always be... [dramatic explosion] a Reaper King Catalyst!
SHEPARD: The weight of such a burden... it must be mine! For this sounds like a Paragon op-
BOLVAR: The Reapers' death rays... sealed my fate. The world of the living can no longer comfort me. Place the Crucible...
ANDERSON: That SOB looks like a husk, I say we kill him.
And then you are presented with a choice of:
No random creepy guy, I can not. (which results in him becoming the Catalyst anyway and Shepard vowing not to tell anybody and then uploading a holo-vid of what happened there to teh extranets)
[Kill him]
and
I have to go.
And regardless of your choice ME4 focuses on pandas being uplifted by salarians to become a dominant race in the galaxy. Deal with it.
Theory Two: Make Love Not Crucibles
When the Catalyst tells you that you have to sacrifice yourself in order to defeat the Reapers and end the Bl invasion, Liara emerges with another solution. All you have to do is impregnate her (or EDI - now that would be the true SYNTHESIS ending) and then kill the Archreaper err I mean Harbinger with her around. If you don't like the idea or if Shepard is female, you have the opportunity to make Joker ("You'll have to forgive me if I close my eyes and think of EDI"), Garrus ("You'll have to forgive me if I close my eyes and think of calibrations") or the Illusive Man ("You'll have to forgive me if I close my eyes and think of Shepard") do the job for you. And then the game pits you against the Harbinger and waves of husks, and you can summon krogan, rachni, geth or thresher maws to help you in that battle. Should be pretty trivial since none of them can shoot fireballs that knock friendlies down (damn you, Irving!)
But that doesn't really matter since ME4 focuses on adventures of some random guy on some random remote colony and the last boss is a pissed-off permanent PMS justicar indoctrinated by a pistol made of red eezo. Anderson merges with Javik and blows up the Citadel, Dumbledore dies and pandas are uplifted anyway.
Theory Three: Reaper Men / a Song of Synthetics and Organics
Shepard is actually not hallucinating somewhere in London, but rather lies in coma since the blast that destroyed the first Normandy and dreaming. With a little help from Cerberus and the Shadow Broker (who is actually a bald eunuch) he/she recovers, beats ME2 again and is court-martialed and executed in front of the crew and the terrified players because, you know, you shouldn't have trusted Petyr Bae the Illusive Man. But don't worry, there's still ME4, and ME5, and all the way to ME7. Liara marries Harbinger and hatches three little Protheans from seemingly inactive lifepods, and names one Shepard. Pandas are still uplifted but then betrayed and slaughtered during a wedding feast because nobody's safe out there since BioWare's got a new writer.
Theory Four: Thank You Shepard But Our Catalyst is in Another Citadel
Self-explanatory. ME4 is the same as ME3 except there are pandas.