Lucy Stillman

As the game progresses, Desmond learns more and more about Lucy. He does this in two ways.

[edit] Conversations

Throughout the game, Desmond can speak to Lucy and get to know her better at the end of each memory segment, after Dr. Vidic leaves the lab. As Desmond talks to Lucy, she starts to tell him a bit about her past.

Lucy explains that during her university career she was ostracised for her scientific beliefs and theories. The criticism continued after university- no scientific organization or academic institute would employ her. Desperate, she was almost ready to give up science altogether. Then she received a call from Dr. Vidic, who told her he agreed with her theories and offered her the chance to work for Abstergo and to prove her theories to be true. The beliefs she was criticized for may have regarded genetic memory. Lucy is portrayed in the game to be knowledgeable about the Animus, so it's likely that, because of her feelings on genetic memory, Vidic contacted her so she could contribute to the creation of the Animus.

Lucy also reveals to Desmond that he is not the only person Abstergo is detaining- she too is a captive. She then tells him a story about how a while back, Abstergo decided to silence her to keep her from speaking about the Animus, but before her assailants could commit her murder, they were ordered to stop by Dr. Warren Vidic. She claims that he saved her life that day, and she tells Desmond not to judge Dr. Vidic so harshly, as he is under a lot of pressure.

[edit] Emails

At various points in the game you can gain access to Lucy's computer and read her emails. Desmond comes upon the codes to Lucy's emails when he finds door codes to the main room in his wardrobe, and Lucy's access pen, which was left on the Animus. It can be speculated that she planted them to give him a better idea of what was going on with Abstergo. However, this is not certain. The codes may have been left there by a previous subject, and the pen left by mistake.

From the messages, you definitely get the idea that she is telling the truth, as she is obviously concerned for her own safety and is trying to find out more information about a previous Abstergo employee who died a while back. This employee is said to have "committed suicide" but the documents relating to the death are being held as classified and are not being released.

In one deleted email, there is a conversation in which Lucy tells another person that she has been delaying the doctor from finding the artefacts and asking for the other person to send a rescue. A strange reply appears to be an attachment, but has random capitalization of letters. When these capitalized letters are put together, they form, "WE WILL BE THERE SOON". Towards the end of the game, a gunfight is heard outside, and Vidic explains that present-day Assassins have come for Desmond. The hidden message was probably a reference to the attack. If so, it would mean Lucy is an assassin, which is also shown by her showing Desmond her left hand and symbolically pulling in her ring finger to have it appear like Altaïr's missing finger, and is spying on Abstergo Industries. The V-neck and collar of her blouse, if turned upside down, are also identical to the Assassin's logo.  At the end of the game, Desmond gains the ability to use Eagle Vision. When Desmond uses this on Lucy, she appears with a blue aura, confirming her to be a trustful ally.

[edit] The Side Story of Leila and Neumann

More spoilers...must include two figures from "bloody mural" here for openers:

The Lorenz Attractor

The Lorenz Attractor, which appears in the middle of the wall over Desmond's bed and is the central focus of the entire "mural" is emblematic of the "butterfly effect". The intricate interweaving of the lines which compose it are paths taken by a particle.

Subject 16 states in the triangle shaped message on the floor that he drained his own body to paint the figures on the floor and walls of the main room where the Animus is located. But had he also used his own blood to paint the wall mural in the sleeping room, he would have bled out - literally - before he finished his work. It is possible that it is Leila's blood used in the wall mural in the sleeping room, done before he painted the messages with his own blood in the Animus room - a murder/suicide.

Spending too long in the Animus is the issue causing it. This seems to be her main reason for concern about Desmond, although it's mentioned very briefly.

Was this Neumann that Vidic mentions in his email to Lucy about "dipping her quill in company ink". Leila operated the Animus before Lucy and probably talked to Subject 16 much as Lucy talks to Desmond (Subject 17) - Neumann's immediate successor. This all must have occurred shortly before Desmond was brought to Abstergo's Lab. Could it be that Leila fell in love with Neumann and was trying to help him and talk to him, and he killed her...then proceeded to paint the bedroom wall with her blood in his desperation and insanity?

Finally, who was Neumann? Strangely enough, a search on the name turns up someone of interest that is significant in relation to all of this. His name was John von Neumann, who died in 1957 (long ago enough for him to have a descendant). He was an Hungarian mathematician who "who made major contributions to a vast range of fields, including set theory, functional analysis, quantum mechanics...continuous geometry, economics and game theory.... He is generally regarded as one of the foremost mathematicians of the 20th century." Wikipedia. We have the Mandlebrot Set - an example of set theory and the repeating overall patterns of history. It is also an example of continuous geometry - a fractal or holographic fragment of a larger whole that is identical to the smaller part. We also have the Lorenz Attractor, which is part of Chaos Theory:

In mathematics, chaos theory describes the behavior of certain dynamical systems – that is, systems whose states evolve with time – that may exhibit dynamics that are highly sensitive to initial conditions (popularly referred to as the butterfly effect). As a result of this sensitivity, which manifests itself as an exponential growth of perturbations in the initial conditions, the behavior of chaotic systems appears to be random. This happens even though these systems are deterministic, meaning that their future dynamics are fully defined by their initial conditions, with no random elements involved. This behavior is known as deterministic chaos, or simply chaos.

Assassins Creed is most certainly a "deterministic" game, in that there can be only one outcome no matter what you do or when you do it. There are probably millions of permutations of activities within it. (This is true of any game worth its salt!) And last, but not least, Mr. Neumann was one of the major developers of game theory.In the second assassins creed lucy betrayes desmond and fails to assassinate him because of vidic the desmond has to chose between vidic or lucy.

[edit] Assassin's Creed II

In Assassin's Creed II, Lucy flees along with Desmond from the Abstergo building to a modern Assassins' hideout.

Lucy with Desmond in the Assassins' hideout.

Lucy with Desmond in the Animus 2.0.