Q. What does the block of writing say?
A. "Artefacts sent to the skies to control all nation, to make us obey a hidden crusade. Do not help them." This message refers directly to Abstergo's plan should they (and they will) get hold of the artefact that you're being used to locate. They plan to send it into space and attach it to a low orbit transmitter to brainwash mankind. In the final battle Altair discovers just what the artefact, the Third Piece of Eden, is capable of. It can make people believe anything, and was responsible for many Biblical illusions such as the parting of the Red Sea (in 'reality' it did not happen - the artefact simply made people think that it did). Subject Sixteen is well aware of Abstergo's plans and asks you not to help them.
Q. What does 12212012 mean?
A. It may be easier if we call it 21122012, for this number's a date. Specifically, 21 December 2012. It's a hugely important date, for it marks the 'end of the world as we know it'. The ancient Mayan civilisations used the Mesoamerican Long Count calendar (incidentally, we use the Gregorian calendar), and a significant event is supposed to take place. In Assassin's Creed this event is obvious, and it also tells us when the game takes place.
Reading through Vidic's emails you'll see that Abstergo must 'launch' on 21 December. It is safe, then, to say that the 'present day' antics take place in September 2012, and that Abstergo wish to launch the satellite on 21/12/2012 to begin the new era in control of mankind.
Q. What about 220.127.116.11.0?
A. This refers to 21/12/2012 again. To be more precise, it is the date written in long count form and marks the beginning of the thirteenth Baktun.
Q. What is the significance of the animal pictures?
A. There are three animals pictures: a hummingbird, a spider and a monkey. All three pictures are drawings of the famous Nazca lines - a series of lines in Peru that, when viewed from above, reveal giant animals. It's probable that the area is home to another ancient artefact, or if not the pictures reveal the location of one.
Q. What are the pyramids about?
A. The step pyramids are a common symbol of Mayan architecture. The Mitchell-Hedges skull was found inside a Mayan temple, and there are more artefacts locked away within the ruins.
Q. What is Yonaguni?
A. Yonaguni is the westernmost island in Japan, and a likely setting for the next game (or at least part of it). It is widely believed that an ancient and advanced civilisation once lived on Yonaguni, and that they suffered a similar fate to Atlantis' people. Buildings found submerged around Yonaguni predate any other known buildings in the world, so expect any Japanese ancestor tales to take place before Assassin's Creed 1.
Q. What is 22:13?
A. Revelations 22:13. "I am the Alpha and the Omega, the First and the Last, the Beginning and the End." There are also a few alphas and omegas scrawled on the giant mural.
Q. What's the eye in the triangle about?
A. Yet another reference to a God. It's a Christian version of the Eye of Providence - the eye of God. The triangle emphasises the Trinity. It's strange that among all the religions and beliefs there are some strong Christian vibes - strange because the game keeps sewing seeds that hint it's a lie.
During the game it's mentioned that Jesus Christ is not the Son of God and that it's a fabrication. The final email also mentions that artefacts related to Christ are probably fictional. And yet we have a couple of Christian symbols and a massively powerful New Testament verse that suggests maybe the opposite is true. Maybe the Piece of Eden has been used not to support a lie about Christ, but to cover up the very truth of the matter.
Q. Emporer Ji... Jing...?
A. "Within Emperor Jiajing'[s] sin and Quetzcoaltz's hunger lies the Answers." Emporer Jiajing was the Emperor of China from 1521 to 1567, and the 11th emperor of the Ming dynasty. He was not a kind emperor, and an internal plot to assassinate him was planned although ultimately failed (note: a possible 'level' in a future Assassin's Creed). He built the Temple of the Sun (notice a theme about the Sun in the paintings around the two rooms) and collected rare materials from around the world. One of these rare materials is almost certainly an artefact.