Second Disaster

"I had hoped you might find this place – and finish our work. But it is too late. You and the Templars have squabbled over our refuse. You have wasted centuries. And so you have lost your chance. You cannot hope to stop the end now, Desmond. Only to survive it."

- Minerva, to Desmond Miles.

Predicted, but ultimately ignored for much of recorded human history, the 2012 coronal mass ejection promised to see the near complete destruction of mankind.

On 21 December 2012, the Assassin Desmond Miles used the Eye to protect the Earth from the Second Disaster, at the cost of his own life, and the release of a vengeful Juno from the Grand Temple.

Predictions
Following the Toba catastrophe, which saw the near complete extinction of both the First Civilization and their human enemies, the three known as the Capitoline Triad: Juno, Jupiter and Minerva, sought to help protect the world from a predicted second event. To this end, the three developed the Vault program, and built the Grand Temple to store their research.

After much experimentation, the three settled on one idea, but before they could bring their plan into action, Minerva and Jupiter learned of Juno's treachery and sealed her within the Grand Temple. Following the eventual extinction of the First Civilization, humanity passed on warning through word-of-mouth, though soon it became mired in myth and legend – ignored by many as superstition.

In 1499, Minerva appeared to Ezio Auditore da Firenze in the Vatican Vault and warned him of the coming disaster, and how to prevent it. Aware that Ezio's descendant Desmond Miles would watch this meeting via the Animus, she addressed the message directly to him. However, instead of finding the temples, Ezio and Niccolo Machiavelli concentrated on unseating the Borgia's control over the Papacy, and left his Apple of Eden for Desmond in the Colosseum Vault. In 1512, Ezio viewed another message for Desmond from Jupiter left in Altaïr Ibn-La'Ahad's Apple.

Even by late 2012, neither the Assassins or the Templars truly knew what was about to occur, although the Templars had their suspicions, having read Minerva's message in the Prophet's Codex, and sought someone with Ezio's genetic memory to locate his Apple.

Juno's machinations
Before she inserted herself into the temple's "mainframe", Juno threw away discs that were left in the Grand Temple for Desmond, by Jupiter and Minerva, so that he had only her words to follow upon his eventual arrival.

Following this, in 1769, Juno used one of the Crystal Balls to converse with the future Assassin Ratonhnhaké:ton; she urged him to join the Order in order to obtain the Grand Temple Key and hide it, so that his descendant, Desmond Miles, might one day find it.

Then, in February 2011, the Assassin Clay Kaczmarek was captured by the Templar front company - Abstergo Industries - for use in their Animus Project. Forced into the Animus, the Bleeding Effect soon overcame Clay, and he found himself unwillingly exploring the memories of his ancestors without the use of the Animus, driving him insane. It was in this induced state that Clay happened upon Juno.

Juno used Clay to pass on the word of the true nature of the coming apocalypse to another Assassin, Desmond Miles, in the hopes that he might be able to reach the Grand Temple and activate the Eye. In order to facilitate this meeting, Juno later manipulated Desmond, who had reached the Colosseum Vault on 11 October 2012, into assassinating his close friend and Assassin colleague Lucy Stillman, and drew him into an induced coma.

Once freed from his coma, and furnished with the knowledge of what he needed to do, Desmond Miles and his companions entered the Grand Temple. After a month, wherein they found themselves forced to locate several batteries for the Temple, as well as the Key itself, the Assassins finally managed to enter the Temple's inner chamber, and on 21 December 2012, approached the Eye.

The freeing of Juno
It was here that the Assassins finally learned the truth about Juno, and what exactly saving the Earth would mean for humanity.

If the Eye was used, the Earth would be saved, but the binds restraining Juno in her prison would be severed, and she would be free to take her perceived vengeance upon humanity. If Desmond let the world burn, however, the cycle would begin anew, and humanity would not learn from the history that was hidden from them; but Juno would remain imprisoned.

Ultimately, Desmond decided that the cost of keeping Juno imprisoned - the near complete extinction of the human race, followed by his legacy being turned to justify mass genocide - was too great, and that at least humanity stood a chance against Juno, following which he activated the Eye.

The Eye then activated what was described as a "global aurora borealis", which shielded the Earth from the worst part of the coronal mass ejection, and ensured the continued survival of modern human life. In doing so however, Desmond sacrificed his own life and subsequently released Juno from her confinement.

Trivia

 * The 2012 coronal mass ejection is closely related to, and based upon, the real world, in which many believed the world would end on 21 December 2012, at the end of the 5,126-year-long cycle in the.