Before Ubisoft decided to kill him off in what some fans still think was one of the worst decisions that has ever been made within the series’ storyline, Desmond Miles was the star of the Assassin’s Creed franchise. In the first game, he is kidnapped by an organization called Abstergo which is the embodiment of the modern day Templars. Although raised to be an Assassin as a kid, Desmond rejected that lifestyle and abandoned his family in pursuit of creating his own destiny. Unfortunately, fate had other plans for him.
At Abstergo, Desmond is forced into a machine called the Animus that allows him to relive the memories of his Assassin ancestors. Abstergo hopes to use the memories of Assassins who interacted with the Pieces of Eden in the past as a way to help locate them in the present. In the first Assassin’s Creed, Desmond relives the memories of his ancestor Altair at the Abstergo facility, but it does not do much to advance the larger plot. Here we are just barely introduced to the Pieces of Eden.
In Assassin’s Creed II, Desmond is moved to a secret Assassin headquarters by a double agent named Lucy who rescued him from Abstergo. We’re also introduced to the Assassin associates Shaun Hastings and Rebecca Crane, who continue to appear throughout the later games. In this Assassin’s Creed, Desmond relives the memories of Ezio and for the first time is able to use a Piece of Eden to receive a direct message from the Precursor Minerva. Though speaking to Ezio, and though all of this is confusing to Ezio, Minerva is aware that Desmond can hear her through Ezio and so, for the most part, she speaks directly to him. She warns him of the coming 2012 solar flare and tells him to seek the Precursor temples.
At the end of Assassin’s Creed: Brotherhood, Desmond communes with a Piece of Eden not through an ancestor’s memory, but by finding one his ancestor Ezio hid within a temple in present day. Through this Piece of Eden, Juno possesses Desmond and uses him to kill Lucy. While this is shocking at first, we eventually find out that she wasn’t a double agent for the Assassins, but rather a triple agent for the Templars, of which Juno was aware. And we also see that Juno conveys a general contempt and hatred for humans that the Precursor Minerva did not, despite the fact that they claim to be saving us together.
At the end of Assassin’s Creed: Revelations, Jupiter communes with Desmond through the Animus. He gives Desmond a little more info on the Precursors and shows him how the First Civilization was destroyed by a solar flare. But at that time, there were barely any Precursors left, and for the most part they died out. At this point in the story, we’ve also been introduced to Desmond’s father, William Miles, who joins Rebecca and Shaun’s efforts.
At the end of Assassin’s Creed III, we see the completion of the Desmond Miles saga. In the Grand Temple, Desmond uses a Piece of Eden to commune with Juno and Minerva. Juno informs Desmond that he has the opportunity to sacrifice his life to save the world from the solar flare. However, Minerva warns that Juno has secretly programmed the Piece of Eden in a way that will allow her consciousness to re-incarnate into the world with the potential to control and enslave human civilization once again, claiming, revenge for the Precursors.
It’s a tough decision to make. However, the way Desmond sees it, if he allows the solar flare to hit and destroy the majority of life on the planet, then there is no hope. He cannot justify the deaths of all those billions of people to himself in any way. Minerva shows him that even though Desmond will survive, the world will rebuild and find peace. But that after his death, the world will fall into the same chaos it was in before and people will use the justification of Desmond’s legacy to commit great evils.
Instead, he believes in humanity. He has faith that if he gives his life to prevent the solar flare from destroying civilization, the remaining Assassins will find a way to save the world from Juno’s sinister plans. And so, in the most tragically heroic moment in the Assassin’s Creed series, Desmond Miles gives his life, freeing Juno and unleashing her upon the world. Some fans suspect that Desmond’s mind may still be alive somewhere, but this has not been confirmed.