I finished Mass Effect 3 and I LOVED it , but (Huge Spoilers)

[Kantor]

coolbeans said:

Kantor said:

coolbeans said:

Kantor said:
The indoctrination may well be the real ending, but if it is, then the ending is unfinished.

I fail to see how it's indoctrination when the Prothean VI scanned you both times and only mentions "indoctrinated one" when Kai Leng enters.

Shepard wasn't indoctrinated at that point. He only becomes indoctrinated at the very end.

That's what I'm confused about though.  After being near Reaper tech throughout 1+2-and even getting zapped with it in the Arrival DLC, what makes the situation different at the end of 3?   Are they trying to say Shepard's strong will allows him/her to 'box in' the indoc. in his/her dreams or what?  

He's standing next to quite literally the entire Reaper army, and he is zapped by Harbinger, the king of the Reapers. This is enough to make even Shepard start to hallucinate.