Great Catastrophe

"The earth shook for days, the fires burned for weeks, and when the ash had settled, less than ten thousand of your kind still lived, and far fewer of ours. But we carried on, together..."

- Jupiter to Desmond Miles.

The Toba catastrophe was an event during human pre-history, which saw the near total extinction of both humanity and the First Civilization, who were involved in a military conflict at the time.

In modern times, the disaster was often misconceived to have been the eruption of a super volcano, but was in actuality caused by a, or solar flare.

Pre-Catastrophe
Embroiled in their war with humanity, the First Civilization did not foresee the coming apocalypse until it was too late; despite this, certain members of the First Civilization worked to find a means of suppressing it - or at least protect future generations from the predicted repeat - by researching ways of preventing the cataclysm within underground Vaults. As stated by Jupiter, they tried six different methods that showed the most potential, but none of them worked.

Disaster and aftermath
The coronal mass ejection hit the Earth just as predicted, flipping the polarity of the Earth's magnetic field and exposing the planet to the Sun's deadly radiation. The entire planet burned; for weeks afterward earthquakes catastrophic blazes ravaged what remained of the planet.

The surface of the earth was rendered barren; less than ten thousand humans and "far fewer" members of the First Civilization survived the catastrophe. In order to recover from the event, the remaining members of the First Civilization and their human creations brought their war to an end and begun to work together to restore life to the planet.

Because their numbers were too few, the First Civilization failed to survive long as an independent species. Humans on the other hand who had been built by the First Civilization "to survive", successfully managed to reconstruct their society and flourished. Over time, the reshaping of the Earth's landscape and geography would eliminate nearly all physical evidence of the First Civilization.