Assassin's Creed: Revelations - Toba Catastrophe - Fall Of The First Civilization

"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 coronal mass ejection, closely related to a solar flare.

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, and earthquakes and catastrophic blazes ravaged what remained of the Earth.
The surface of the earth was rendered barren, and 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.