Vatican Vault
The Vault is one of the "Temples" left by Those Who Came Before, but their exact purpose is still under speculation. Minerva's message is that the Vault's contain some sort of assistance or research in staving of a repeat of the Catastrophe that has occurred before.
Originally, it was thought by the Spaniard that the Vault contained the living God, and he wished to overthrow him and control everything. What WAS found in the Vault however, was quite different.
It appears that only a combination of different Pieces of Eden can open it, and are built to only allow specific people to enter, such as Ezio, who was named a "prophet". In Assassin's Creed II, Ezio enters the vault under the Vatican and opens the Vault door by holding the staff which has a Piece of Eden attached to it. In the Vatican vault there are images on the wall that only appear when Ezio comes near them detailing other Vault's locations; this is the true "data" of Minerva's genetic transmission. 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.
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. She begins to speak of how she is not a God, but simply came before humans, being more advanced in technology. 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.