If the "breath" scene is to be cannon ((and its been confirmed that it IS sheperd)) they would need to mix in IT of sheperd at some point, maybe leviathan took control of shepard as they did the rush for the transport beam and made him think he was up in the citidel.
this could be leviathans big test to see what shepard would do and the image of harbinger taking off was the last "real" image before he slipped into a type of IT hypnosis, what he thinks he see's is real is in fact just a dreamstate coma, leviathan is wondering between themselves what should we do.
they then agreed to see what shepard would choose, let him get up to the citidel, use images, people and locations in his memory to see what he would do, if he picks destroy then they show him in his mind what the outcome may be, if he picked synthasis they show him, control they showed him.
the flaw in the 3 endings is that 2 cants be done because it would actually be impossible as his body would be destryed before his mind can do anything ..... the last is him with a bigass gun.
so for the IT naysayers just think about the endings choices and remember that 2 of them are impossible.
control requires your mind but your destroyed before you can think.
synthisis your body is vaporized by the power beam from the crucible so that in itself is impossible because thats just a power transfer system and does nothing.
but the destroy option gives you a chance os survival because your shooting the hell out of what could be a power node which forces a full on shutdown of all of harbiners systems.
BUT the last option could be the new REAL ending ... rejecting all of the catalyts choices this was a new option and would not have been put in to apeese us, there would have been a reason for it if you think about it.
also remember what edi asked on the normandy, shepard basicly told edi its all up to her and not have someone make the choice for her, so the catylst gives shepard the choices because it does not know what to do, so we reject them and this may cause a cascade failure of ALL of the catylsts and harbingers systems as there now stuck in a recursive algorithm which uses up more and more of the reapers memory cores, over loading there cpu's untill they eventually ((and literly)) crash and shutdown which would then leave them ALL open for a formating and reinstallation of a new operating system ......... maybe linux since we all know they all run on apples IOS as we all know apple want to control the world
but again just THINK about it