User blog comment:The Milkman/Indoctrination Theorists Say the Darndest Things, Part II/@comment-5830255-20121205074259/@comment-4237253-20121205153121

I think he means that the exposure to Reaper artefacts over time eventually set Shepard up. Then, the Reapers initiate the "final step" right when Shepard is close to the beam. I didn't know the there was even a final step, or that indoctrination stacked, but there you have it.