The Codex 17: The Flames...

Of all the things I've seen, none troubles me more than the image of the flames... Pillars so tall they seemed to pierce the heavens. The ground rumbled and shuddered. Mountains split and crack. Great metal towers splintered, their innards strewn about the ground... And everywhere there was screaming. A chorus so terrible that even now I feel its echoes still.

What is this madness I have seen? Is it them, I wonder? Those who came before... Is this where they went? Into the fire? Into the dust? Perhaps this destructive power is what the Templars seek. That they might hold it over us a command devotion. What hope would we have, then, if they held such darkness in their hands – that they could murder the world...

Contemporary: Subject 16 explained how "toba was not a volcano," in his glyph puzzle about the sun. Minerva herself explained the whole thing. How those who came before fought a war against their human slaves (is slaves a right word? machines perhaps?). But in the meantime, a cataclysm involving the sun set the heavens on fire and destroyed both sides. The survivors were "those who knew to turn away from war." They built temples for the future. Minerva ends with giving Desmond the task of finding these temples and warns him to guard against the "cross." 
I think it is interesting she specifically warns him of the Templars. What do the Templars know of the cataclysm. They had Subject 16 and some of his session records went missing. Could the Templars know of the catastrophe? Could they be planning to use the next Toba catastrophe to their advantage? Could, like Altair suggests, they know how to cause one? And if they know how to make one occur, what does that say about the cause of the first?