The Assassins last hope is Desmond Miles, who comes from a long line of Assassins
The Assassins Creed series has centered on protagonist Desmond Miles. Each of the games in the series thus far has been predicated on going into Desmonds past to learn more about the war between the Templars and the Assassins, the Pieces of Eden, and the First Civilization. Its believed Desmond may have some genetic ties to the First Civilization, and thats why hes been chosen to help try to avert the world-ending catastrophe predicted to happen on December 21, 2012.
Desmond initially tried to get away from the Assassin Brotherhood, and ran from his compound during his formative years. Desmond was able to stay off the grid until 2012 when Abstergo discovered him. Realizing how important Miles was to discovering more Pieces of Eden, the Templar front captured him for their own devious purposes.
But Abstergo captured Desmond before he could realize his potential
The first Assassins Creed finds Desmond in the clutches of Abstergo, forced to undergo Animus treatments while in captivity. In custody, Desmond meets Dr. Warren Vidic, head of genetic research at Abstergo (and member of the Templar Inner Sanctum), and Lucy Stillman, Vidics assistant (and undercover Assassin).
Vidic keeps close tabs on Desmond, as he believes his genetic ancestry will be the key to finding another key Piece of Eden for the Templars. He's right.
Abstergo used the Animus to research Desmonds ancestry
While undergoing Animus sessions at Abstergo, Desmond was put into the genetic memories of Altair Ibn-La'Ahad, a Syrian Assassin who battled the Templars during the Crusades. At first, Desmond struggled with the memory hunting within the Animus, which caused Vidic and Stillman to argue about how much exposure Miles had to the device. The previous user, Subject 16, was driven insane by prolonged use, and Stillman advocated for Desmonds time in the Animus to be measured. Vidic conceded, and shortly thereafter, Desmond had a breakthrough.
While reliving Altairs experiences, Desmond saw a map with key locations of valuable Pieces of Eden marked out, which is exactly what Abstergo was hoping to find. Vidic wanted to dispose of Desmond once the map was discovered, but Lucy advocated for his safety, indicating Desmond may be useful again in the future.
until Lucy Stillman, Shaun Hastings, and Rebecca Crane helped Desmond escape
After Desmond outlived his usefulness at Abstergo, Lucy (a spy for the Assassins) and several other Assassins put plans into motion to help him escape. After convincing Vidic to keep Desmond around, Lucy quickly threw Desmond into the Animus one more time. There, Desmond was linked to an ancestor who also had ties to Subject 16, Ezio Auditore da Firenze. Once the new genetic link was set up, Lucy grabbed the Animus hard drive, and escaped with Desmond to meet up with Hastings and Crane.
Once at the new Assassin hideout, Desmond was introduced to the Animus 2.0. With Cranes and Hastings help, Desmond would be able to not only live out the genetic memories of Ezio to help the Assassins find more clues to help stop the Templars, but he would also be able to learn all of Ezios skills thanks to the Bleeding Effect. Now fully aware of the stakes, Desmond willingly entered the Animus 2.0, and began the path to being humanitys potential savior.
Desmond also had some help from Abstergos previous victim: Subject 16
Subject 16s prolonged exposure to the Animus drove him crazy, and led to his committing "suicide" (psst, it wasn't really suicide). Before he did "kill himself," Subject 16 implanted his memory into the Animus core, and made it so only his successor would be able to access that portion of the core. Subject 16 was a direct descendent of Adam, which meant he had prolonged knowledge of the Apple of Eden, and was of great importance to Abstergo before his paranoia got the best of him.
Though Subject 16s influence on Desmond in the first Assassin's Creed was minimal, Desmond was aided greatly by Subject 16 during his time in Ezios memories. This was due to Subject 16s imprint still being part of the memory core stolen from Abstergo, and implanted into the Animus 2.0. Subject 16 had left some broken and hidden code in the core, and Desmond was able to find and explore these areas to learn more about the ongoing battle between the Assassins and Templars, as well as the truth about Adam, Eve, and the First Civilization.
He has lived through the lives of two of his ancestors so far
There have been a handful of Assassins Creed titles released, but Desmond has only gone into the genetic memories of two of his ancestors: Altair and Ezio. Desmonds time with Altair taught him a lot about the way the conflict between the Assassins and Templars has worked throughout time, and introduced him to the modern day face of his foes at Abstergo. Desmonds time with Ezio has proven far more valuable. He has lived through a larger portion of Ezios life, and has thus learned more skills, more information on the history of the feud, and conversed with members of the First Civilization.
While living through the memories of Ezio, Desmond was also able to put the Assassins back on track in the war on the Templars by discovering one of the remaining Apples of Eden.
and managed to find an Apple of Eden
There are believed to be five remaining Apples of Eden in the world at the onset of Assassins Creed. Abstergo has one, but lost another during a tragic event in Denver that still remains shrouded in mystery. Even though Desmond was able to wield the power of the Apples of Eden both Altair and Ezio had found during their lifetimes, these Apples were still missing in the modern day. The Assassins hadnt had as much luck until Desmond was able to discover where Ezio hid the Apple of Eden he found centuries ago.
Buried in a hidden vault deep in the catacombs of the Colosseum, Desmond found the Apple of Eden. While in the vault, Desmond was contacted by Juno, one of the members of the First Civilization. Juno warned Desmond again of the cataclysmic event that was approaching, and that there was a traitor in his midst.
After touching the Apple, Desmond killed his BFF Lucy, and fell into a coma
Once Desmond touched the Apple of Eden in the vault, Juno possessed him. Time stopped, and Desmond found himself helplessly watching as Juno controlled his body, directing it to stab Lucy.
When Juno released Desmond from her possession, Lucy was dead, and Shaun and Rebecca could only look on in horror. Overwhelmed with the power of the Apple, the prolonged Animus times, and the shock of having just murdered one of his closest friends while being possessed by an advanced ancient being, Desmond slipped into a coma.
but its okay because Lucy was totally a Templar spy
Abstergo and Dr. Vidic planned out every single moment of Lucys friendship with Desmond (if you missed this during the series we understand--it was tucked away in Revelations DLC). Dubbed Project Siren, the operation for Lucy to infiltrate the Assassins by way of befriending Desmond was almost a success. Once Desmond had gotten his hands on the Apple, Lucy was going to betray the team to the Templars, and return to Vidics side. No one had planned for Junos intervention however, and Abstergos grand plan fell apart at the very last moment.
Once Desmond had slipped into his coma, Shaun and Rebecca hastily contacted one of the Assassin leaders, who just so happened to be Desmond's father. Mr. Miles advised putting Desmond back into the Animus to try and revive his consciousness. The group has been on the run ever since, trying to stay one step ahead of Abstergo and the Templars while Desmond recovered.
Now Desmond is totes better, and is ready to save the world
The events of Assassins Creed: Revelations all occur while a comatose Desmond is in the Animus. There he finally meets Subject 16 face-to-virtual-face. Seeing just how close Desmond is to losing his mind to the Animus, Subject 16 reconstitutes himself in the virtual reality construct, and helps Desmond not only see through Ezios final days, but also helps Desmond put his mind back together. Being in a coma while in the Animus is very bad, you see, so Subject 16 and Desmond have to work fast before Desmonds consciousness is absorbed into the Animus, and his living body becomes brain-dead.
We learned a lot about Desmonds life while he struggled to put the pieces back together, including how he spent his time between leaving the Assassin compound and being captured by Abstergo. With the help of Subject 16, Desmond is able to put back his shattered mind, escape the Animus, and whats more, leave with knowledge of how to use the Apple of Eden to stop the Templar Order.