I feel I should point out, I posted the part of my interpretation of this new development pertaining to Minerva's identity . Needless to say, any theory that Minerva is anything but a technology-based entity is losing ground, fast.
I think that so far we've overlooked some items of importance here. First: the title of that page is "Entoptical Phenomena". Now, if you're like me, your first question is "What in the world does entoptical mean?". Even if you didn't wonder about that, is some more info. Basically, it means a condition is which you see something within your eyeball itself. One example is "phosphenes", the pretty little patterns you see when you close your eyes too tightly. But we can extrapolate that to mean "seeing something inside yourself" and/or "seeing something you don't normally see".
Now look at the URL:
http://www.hylobatidae.org/minerva/traitor.shtml. Hmm, a traitor? Who could that be? Well, we know Minerva has access to some Combine security protocols, and even calls herself a "discarded piece of shit" and a " manufactured war criminal". Perhaps Minerva turned her back on the Combine and/or on humanity. Remember, she claims to have helped discover teleport technology - maybe she had something to do with the Combine finding Earth, making her an accidental traitor, or perhaps she betrayed us all in return for being made into... whatever she is now. Maybe she even betrayed us in the hopes of saving herself, or something else (perhaps whatever was beyond the portal), and now regrets turning her back on her home.
We can also determine that Minerva is, at least in part, working with Combine data - note the presence of City 44's identification code. But then, that's really nothing new for her, is it now? Notice as well that the location circles could represent two things: places Minerva is interested in, or places where Minerva has been found. It could be a to-do list, of sorts, but to me it seems a bit short to be so. Perhaps this is a sort of Combine tracking effort - they're watching Minerva, seeing what she does. Maybe they want to know what she is and what her goals are as badly as we do, but she's caught on.
As for what all these clever observations mean, I will state that for now, I don't know. We must be thorough, as we're by no means sure how long this will have to last us. If OoT is as work-intensive as it looks, we may have a while to wait.
