Loved it! Really enjoyed the portal-like theming of the omniscient overlord deceiving you, and unraveling the mystery as it goes. I think you could do a lot with the format too, you took a classic puzzle format and add that sort of autonomous independence and 3rd person section, it could be expanded into something really cool.
One thing, I noticed the 'mute music' button at the beginning but (at least on my computer) there was no music and no sound effects. Not sure if that was because you ran out of time or it should be in there and it's a bug.
Great job!