Bleeding effect
Prolonged exposure to the Animus caused a 'Bleeding Effect' within Subject Sixteen's genetic structure. The result was a blending of genetic and real-time memory.
―Lucy Stillman's e-mail to Warren Vidic
The bleeding effect is a disorder caused by overexposure to the Animus, suggested by Lucy Stillman to be similar to 'certain forms of multiple personality and delusional disorders'. With increasing exposure, subjects begin to experience a blending of their own real-time memories and their genetic memories, leading to difficulty in distinguishing the two, and ultimately mental breakdown. The effect is suffered notably by Subject 16 and Desmond Miles.
Due to the bleeding effect, Desmond develops the ability to use Eagle Vision, allowing him to see Subject 16's messages.
Symptoms
Though the specific symptoms may vary from subject to subject, the end result is the same: they lose their minds.
―Lucy Stillman's email to Warren Vidic
Desmond gains the fighting and free-running abilities of his ancestors, as well as the ability to use Eagle Vision. This is followed by hallucinations; in Assassin's Creed II, Desmond is told that as long as the visions are shorter than thirty seconds, "he'll be fine". They start out ghost-like and indistinct, but become longer and more vivid, at one point causing Desmond to black out.
Subject 16, known as an extreme case, is seldom described before his breakdown. In his messages to Desmond through the glyphs, he has difficulty remembering who he is and what year it is; however, he thinks clearly enough to keep the goal of revealing The Truth in mind, and to leave messages and clues to do so. He becomes increasingly obsessed with this, leading him to drain his own blood to write with.
Assassin's Creed
The bleeding effect is at first only hinted at, with Lucy and Vidic implying that using the Animus for prolonged periods was dangerous. Later, Lucy's email to Vidic describes it in much more detail: having been forced to use the Animus for days at a time, Subject 16 gradually became unable to control the bleeding effect, and was driven to insanity by the genetic memories he experienced outside the Animus. Eventually, after writing warnings to future subjects in his own blood, Subject 16 committed suicide.
Meanwhile, by the end of Assassin's Creed the bleeding effect is starting to show it's side-effects with Desmond, allowing him to use Eagle Vision outside of the Animus.
Assassin's Creed II
After their escape from Abstergo, Lucy attempts to use the bleeding effect to train Desmond as an assassin much more quickly than would otherwise be possible. He is quickly able to learn skills such as Free Running in the Animus by following the life of Ezio. The bleeding effect gets progressively worse and Desmond begins to hallucinate about his other ancestor Altaïr, who he recollected memories from in the first Animus. This allowed him to see how Altaïr chasing Maria up to a tower, where the conception of their first child happened. Despite the side-effects Desmond continues to use the Animus.
Subject 16, apparently able to see Abstergo's past plots through the bleeding effect, leaves an intricate trail of evidence through the memories of his and Desmond's common ancestor, Ezio.