User blog comment:AdmiralPedro1stFleet/Goodbye Indoctrination and Hello Beings of Light/@comment-65.87.105.3-20120727160544/@comment-72.87.179.46-20130102061443

Catalysts words to shepard "It is now in your power to destroy us. But be warned: others will be destroyed as well. The Crucible will not discriminate. All synthetics will be targeted. Even you are partly synthetic..." Nowhere in there did it tell shepard you will die. It's a warning.

Also with the addition of Leviathan i have become skeptical whether the reapers actually were indoctrinating the Rachni since there weren't ravagers reported at the time.

Shepard is not Indoctrinated, his dreams are nightmares for losing people. (Depending on the choices there are: Akuze, Torphan, Eden Prime, Asteroid X57, Virmire, Feros, the Suicide Mission, etc.) Again he is not Indoctrinated.