The problem with the whole mystery is really that most of the findings were stumbled upon. It wasn't a series of observations or one clue leading to the other that lead to any major discovery. The only major thing that has been found are the UFOs (found by accident when players were flying and diving around randomly) and the Bigfoot/Beast easter egg (solved with the help of coders).

The rest of the theories that have been floating around regarding the moon, the Observatory, the Altruist Cult, the Epsilon Program, Fort Zancudo, Humane Labs, Mt. Gordo, the T01/02 doors and all the rest of it are just that, theories. There is nothing in the game that actually suggests that any of those things are part of a mystery that can be solved. It's all been put together by fans who find odd locations and then tie them together either with something from real life or something like an Epsilon Tract. But then it just goes nowhere.

The last big things I can remember were the golden/big foot peyotes and discovering that bigfoot had some sort of a "sonar". This eventually led to discovering "The Beast".