User blog comment:N7EagleEye/New Mass Effect 4 Details/@comment-79.112.179.186-20130603214045/@comment-10440824-20130604233942

The theory behind the indoctrination theory makes perfect sense. If you've played all the games that is.

In Mass Effect 1, The Rachni queen talks about dreams of oily shadows(Like the ones Shepard has with the kid)

The story in itself along with the secondary enemies makes sense.

In Mass Effect 1, the evil guy Saren wanted to do exactly what you decided to do Lily. He wanted to have synthesis.

In Mass Effect 3, the illusive man wants to take control over the reapers for himself and the human race.

What did they have in common? They were indoctrinated. SO! In the end you have 3 options, two which were chosen by indoctrinated people and one that would end it all now.

You don't sacrifice anything in the story by picking synthesis or control. Only means the Reapers will win, because you have been indoctrinated.