Vatican Vault
The Vault is one of the "Temples" left by Those Who Came Before, located underneath the Sistine Chapel in Rome. The exact purpose of the Vault and the other Temples is still unknown. Minerva's message implies that the Vault's contain some sort of assistance or research in staving of a repeat of the Catastrophe that has occurred before.
It appears that only a combination of different Pieces of Eden can open it; likewise, only specific people seem to be able to enter. Recognized as a "prophet", Ezio Auditore da Firenze was able to enter the Vault by using the the Staff in conjunction with a Piece of Eden. The Vault contains images on the wall that only appear when Ezio comes near them, presumably detailing the other Vaults' locations.
Originally, it was thought by Rodrigo Borgia that the Vault contained the living God, and he wished to overthrow him and control everything. However, the Vault actually contains the sole survivor of Those Who Came Before, Minerva. By her own admission, she is not a God, but a member of a highly advanced race that came before humans. She then says of how 'those who came before' created humans, but faced rebellion( seen in subject 16's truth video). She explains how both the humans, now free, and those who came before, fought a war. She states that she is the last of those who came before. Though those who came before were powerful, the humans had larger numbers, as Minerva described it. Then, after this, she speaks of a great geological disaster that wiped out a great portion of life on earth, caused by the sun, and that those who came before built temples all over the world, like the vault, that could prevent the disaster happening again. Throughout the speech, Ezio appears confused as to what Minerva is talking about, as she admits that she is not talking to him, but through him. She then says,'The rest is up to you, Desmond' seemingly knowing that Desmond would access the memory centuries later in the Animus (noted by the fact that Minerva would always look straight at the camera and never Ezio unless she directly addresses him). Minerva says, that as the prophet, Ezio has done his part. The 'hologram' disappears, leaving both Desmond and Ezio confused, while Ezio shouting that he has so many questions, but said questions were unfortunately not answered.
When Ezio opens the vault, dozens of what seem to be cuneiform runes or glyphs of some kind light up all around him, and an image of Minerva appears in a holographic manner.
Notes
- We can clearly see a step pyramid so there's the possibility of a Vault in Mesoamerica or a ziggurat of Mesopotamia or even the ancient Temple of Borobudur in Indonesia.