User blog comment:AdmiralPedro1stFleet/Goodbye Indoctrination and Hello Beings of Light/@comment-65.87.105.3-20120727160544/@comment-24174486-20120727203335

"what the hell is he even doing in the Crucible?"

The Catalyst is on the Citadel, which the Crucible uses to extend its range via the mass relay network.

"Therefore a Being of Light has no business showing up and explaining to you how to use a human constructed device, which supposedly Shepard should already know how to activate"

The Crucible wasn't constructed by just humans. It's also an ancient device that they have no information on the functionality of. All they know is that the Protheans attempted to use it to stop the Reapers, so they're placing their faith and hope into the Crucible stopping the Reapers even though they have no idea how it is supposed to stop the Reapers.

"telling you: 'Hey guess what? While you were working your way up here, I conveniently installed these three options!' "

The Catalyst doesn't "install" those options. Your options are based on your Effective Military Strength, essentially how much work you've had done on the Crucible. It merely tells you what you can do with the Crucible: use it to destroy the Reapers as you sought to do, control them as the Illusive Man believed could be done, or take the Catalyst's solution of Synthesis.

"Also, the 'Being of Light' lied right in your face telling you that if you destroy the Reapers, you die too, yet if you choose destroy... Shepard lives?"

The Catalyst may have believed that Shepard would die if they chose Destroy. It may have been mistakened. The Catalyst is not presented as an infallible figure.

The biggest problem with the Indoctrination Theory is the number of characters who point out that Shepard is not indoctrinated. The Catalyst points out that the Illusive Man would have been unable to control the Reapers as he was already under their control; Shepard can do so, thus he must not be indoctrinated. Even before that, Vendetta does not say that Shepard is indoctrinated—the VI is shown to be able to detect indoctrinated people near it, based on how it detects Kai Leng on Thessia.