Subject 16 Warns Desmond of Lucy's Betrayal! + Analysis : https://youtu.be/VcYIxI_6h1s
3Note : I did an extensive analysis on the Enigmatic Epilogue of AC Brotherhood here - https://youtu.be/VcYIxI_6h1s
- WHY DID LUCY STILLMAN BETRAY DESMOND MILES & THE ASSASSINS? [In depth Quora discussions added.]
All of this traces back to the time when William Miles (Desmond's Father) gave Lucy Stillman and Clay Kaczmarek (Subject 16) a mission to infiltrate Abstergo and collect their data. Years of isolation from her fellow assassins while working undercover at Abstergo, along with William Miles' WITHDRAWN,COLD AND CARELESS PERSONALITY, drove Lucy into the Templars' arms. Warren Vidic, her boss at Abstergo, offered her protection and guidance, the two things she thought William was withholding from her.
It was set into motion that a new test subject would be needed to find Ezio Auditore’s Apple of Eden, due to Subject Sixteen’s deteriorating health, William’s son Desmond was chosen. As soon as Desmond started suffering from the Bleeding Effect, Warren Vidic and Lucy Stillman deviced a plan ( "PROJECT SIREN" ) for Desmond and Lucy's escape from Abstergo, so that they can get the data they required in the remaining time at a faster rate.
PROJECT SIREN'S FAILURE :
According to the plan, Lucy would help Desmond “escape” and continue looking for the Apple with Shaun and Rebecca, to make Desmond feel safer with other assassin’s, thus speeding up his Animus cycles.
When Clay Kaczmarek (Subject Sixteen) discovered her and Vidic’s plans for Desmond, he was locked away. Lucy still continued to protect Clay, but refused to let him leave, or make contact with the other Assassins. Clay’s health got worse, so he followed Juno's advice & decided to take his own life [Juno's so GRIM man...] But before that, Clay Kaczmarek (Subject 16) hacks into the Animus and plants himself into it. Soon he started programming messages inside the Animus, and wrote the cryptic symbols on the walls in his own blood right before his suicide, In an attempt to warn Desmond not to trust Lucy.
"I am with you until the end. Find me in the darkness."
―Clay Kaczmarek to Desmond Miles
Lucy's Primary motive WASN'T to hurt Desmond or anyone, but to recover the Apple of Eden for the Templars. Since the Assassins DID have a motive to recover the Apple of Eden, though it WASN'T A PRIMARY, their main goal was to "protect" it from Templar order and recover IF necessary. Lucy Stillman betrayed the Assassins because she always WAS a part of the Templars. If possible, her secondary motive wasn't to kill Desmond, but to transport him from Abstergo to another location and use him to locate the Apple of Eden. She was a sort of spy, a HIGHLY DECEPTIVE but a BELIEVABLE one. She really never had no real interest in the Assassins besides locating the Apple and killing anyone who got in her way, besides Desmond, as she could have used him as a resource or bait to get the Apple for the Templars. Lucy was in contact with Warren Vidic THROUGHOUT the events of Assassin’s Creed 2 and Brotherhood.
But ULTIMATELY that Plan failed and backfired. Juno sort of pulled an UNO REVERSE on the Templars as She made Desmond kill Lucy, while the Assassins got the Apple. So basically Assassins used Abstergo to retrieve the Apple of Eden. If not was for Juno, they would have lost it to the Templars. But Juno did it for her own selfish reasons.
In Conclusion, Lucy was just a sleeper agent for the templar just like Daniel Cross (Subject 4). If you want to know more about Lucy and Daniel's background story, you should play the DLC for Assassin's Creed: Revelation. I believe the DLC is called "The Lost Archives"