The theory is specifically that Shepard is undergoing slow indoctrination, and I'm willing to except it's been happening ever since the first mission on Edan Prime in the first Mass Effect.
It would make sense that the longer you play (the more you do), the longer you are exposed to the reapers, the greater their influence is over you.
If you recall there was the option to get Saren to kill himself even when he was so heavily indoctrinated.
I really bought into the theory when I got an email in game about the asari scientist I saved on Vermire killing a bunch of asari diplomats.
It would make sense that the longer you play (the more you do), the longer you are exposed to the reapers, the greater their influence is over you.
If you recall there was the option to get Saren to kill himself even when he was so heavily indoctrinated.
I really bought into the theory when I got an email in game about the asari scientist I saved on Vermire killing a bunch of asari diplomats.