The son of Harold Kaczmarek and his wife, Clay was destined, in his father’s eyes, to follow in the family footsteps and become an engineer. From an early age, Clay showed signs of desiring more for himself; at one point saying to his father that he wanted to become an astronaut. As he became older, Clay’s interests began to differ greatly from his father’s hopes, causing a rift between the two.
At some point prior to 2007, Clay succeeded in gaining entrance to a college on an engineering degree, though his father was disappointed that it was not at one of the top-tier institutions. Dejected, Clay secretly began to visit a psychiatrist to discuss his feelings.
Around this time, Clay was approached by William Miles, a member of the Assassin Order, and was offered an induction into the Brotherhood, which he passed, without the knowledge of his father. Following this, Clay’s psychiatrist noticed a marked improvement in his attitude, behavior and outlook, though he was oblivious as to the reasons why.
From that point on, Clay maintained limited contact with his father – whose business was suffering due to the economic downturn in early 2010 – occasionally sending checks to help support the family. His father’s over-dependency soon drove both Clay and his mother away, leaving Harold on his own.
Clay Kaczmarek had a rich and varied ancestry, which quickly caught the attention of Abstergo Industries. Whilst his immediate ancestors lived relatively normal lives, with many on his father’s side of the family taking jobs in engineering, Clay was most notably a direct descendant of Adam; one of the first humans, alongside Eve, who rose in rebellion against the First Civilization.
As Adam was a child of both a human and a member of the First Civilization, Clay had a notable concentration of First Civilization genes in his blood. Clay also had ancestors in ancient Africa, in the Roman forum and in the Far East. Of particular interest to Abstergo was his relation to the Italian House of Auditore, founded by Domenico Auditore in the early 14th century.
His Auditore bloodline ended with Ezio Auditore da Firenze, as Clay’s next ancestor was an illegitimate child. One of his ancestors was also connected with an unknown Queen Isabella, another with Jean de La Fontaine, whilst another participated in the Battle of Gettysburg during the United States Civil War.
In 2010, William gave Clay the task of infiltrating the Templar front organization, Abstergo Industries. His job was to access the personal computer of Alan Rikkin, the company’s CEO, and uncover details surrounding the secretive “Animus project”.
Succeeding in his efforts, Clay returned to the Assassins with a copy of an e-mail revealing the amount of funding being invested in the project, as well as the identity of the project lead, Dr. Warren Vidic, and the location of his new facility in Italy.
Spurred on by this success, the Assassins decided to plant Clay deeper into Abstergo, this time as a test subject of Dr. Vidic’s program. He was informed that a member of his team was a mole who was already deep inside Abstergo; one who had been raised outside of the Order, and who had all ties with them cut: Lucy Stillman. Assured that when the time came, she would aid in his escape, Clay agreed to the plan.
On 1 February 2011, Clay was captured by Abstergo’s Lineage Discovery and Acquisition team and inducted into the Animus project as Subject 16. Held within the Abstergo laboratory by Dr. Vidic, Clay was forced to relive the memories of his ancestors, particularly Ezio Auditore da Firenze, for dangerously long periods at a time. Throughout this, Vidic kept the true purpose of their genetic explorations a secret, though Clay soon realized that their efforts were focused on locating a mythical “Apple of Eden”.
When Clay inquired about this, Vidic threateningly responded that he could not reasonably expect to be released if he knew what they truly sought. Later, William was able to contact Clay and told him to focus on his task; that when the time came, Lucy would rescue him, as they were a team. Clay gathered a new sense of purpose after Vidic discovered that he was a direct descendant of Adam, the biblical figure.
Adam’s exposure to the knowledge contained within the Apple of Eden was passed onto Clay as their personalities merged. Thus Clay discovered the ancient secrets of the Assassins, the First Civilization and the true purpose of the Animus project and decided that it was time for him to escape.
Unfortunately, by this point, his over-exposure to the Animus had resulted in him suffering from the “Bleeding Effect”, and he soon found himself unwillingly exploring the memories of his ancestors without the use of the Animus. Clay had to act before his mind disappeared entirely. Using his computer engineering skills, he hacked into the Animus, depositing research stolen from Abstergo and his own revelations into the memory core, for his successor to discover. He also synched himself with the Animus, uploading a copy of his personality into the network.
During one of his Animus experiences experiences, Clay found himself conversing with a figure calling herself Juno, a First Civilization member. Clay reacted angrily when he was informed that his death was nigh and that his purpose from then on was to deliver a message to his eventual successor, Desmond Miles.
In order to convince him of the necessity, Juno revealed that the years of loneliness and abandonment visited upon Lucy by the Assassin Order, so that she might better infiltrate the Templars, had in actuality turned her against them; her mission being to aid the Assassins in the discovery of the Apple, before returning it to the Templars. This betrayal shocked Clay, and brought him to the realization of his place in future events.
After a while, Lucy discovered that Clay knew the truth about her true intentions and attempted to explain her actions, saying that William and the rest of the Order cared little for the lives that they destroyed in the pursuit of their goals, whereas the Templars did.
Knowing she could not sway him, Lucy stated that she would keep the promise she had made to protect Clay, hiding the evidence of his new-found knowledge from Vidic, but that she could no longer afford to let him leave. Faced with no other option, Clay realized that there was only one way to get his message to Desmond.
For weeks, Clay planned his suicide down to the most minute detail, biding his time and preparing his message, all the while enduring the repeated attempts by Vidic to uncover the location of the Apple of Eden. Eventually, Clay managed to create an artificial construct of himself inside the Animus, through hacking the machine during the night, and split it into thirty pieces to be united by his successor, as well as sending one final e-mail to his father.
The next day, Clay killed himself by slitting his wrists with a ball-point pen and draining his blood out of his body, in order to paint several cryptic messages in the rooms where he was being kept, hoping to ensure his successor recovered the message that he had died to pass on. After his death, Abstergo dumped his body in the Tiber river in Rome. Not long after, Desmond Miles was abducted by Abstergo and forced into the Animus project. In time, he and Lucy escaped from Abstergo, finding their way to an Assassin hideout nearby, wherein he would begin his own explorations of Ezio Auditore’s memories.
During these investigations, the Assassins learned how Clay had managed to hack Abstergo’s Animus before his death, and that in doing so, he had placed twenty glyphs throughout the Animus system, which were subsequently rendered in the visual memories. These encrypted files, which had been saved onto the Abstergo Animus’ memory core that Lucy had stolen, were later unknowingly transferred to Rebecca Crane’s Animus 2.0. After decrypting all twenty files, the Assassins were rewarded with a genetic memory marked “date classified BCE”.
The video showed two freerunners, primordial Adam and Eve, climbing a large glass structure with an Apple of Eden in hand. Following their escape from the hideout, Desmond, Lucy, Rebecca and Shaun Hastings retreated to the last Assassin safe-house in Italy, the Villa Auditore in Monteriggioni. While there, during their exploration of some of Ezio’s later memories, it was discovered that Clay had left ten more glyphs, which corresponded with locations in Renaissance Rome. Upon visiting these indicated landmarks, Desmond discovered several rifts in the Animus programming.
Within each, Desmond solved a cluster puzzle, which then unlocked a piece of a file. Upon compiling them, they revealed a distorted video with the message “the miracle is in the execution”, suggesting that, unlike the video hidden in the Glyphs, the Rifts instead concealed an executable file. Upon accessing it, Desmond found himself in an unknown area within the Animus, and was able to run through a long virtual maze, similar to those within the Animus Virtual Training Program.
At the end of the maze, he found a wire-frame model of Clay, partially broken and made of computing code. Clay told Desmond that all hope was lost, and that he needed to go to Eden to find a woman named Eve. Before vanishing, Clay told Desmond to find him in the darkness.
Eventually, Desmond and his allies located Ezio’s Apple of Eden, hidden in the Colosseum Vault. It was here that Desmond met Juno for the first time, and where he was influenced into killing Lucy, despite her betrayal not yet having become apparent to her companions. As a result of this, Desmond slipped into a coma and was returned by William to the Animus to support his mental state. When he awoke, Desmond was greeted by the digital construct Clay had inserted into the Animus.
He informed Desmond that they were in a safe mode of the Animus’ software, and he offered his successor advice on how to escape; telling Desmond that he needed to create a Synch Nexus and clearly separate his memories from those of Ezio and Altaïr Ibn-La’Ahad. Since Desmond’s teammates could not contact him, Clay took Shaun’s place as the writer of the Animus database entries. He made an entry about himself, revealing his actual name to Desmond, and he told him how they were distant cousins by virtue of their joint descent from Ezio.
On Animus Island, Clay also mentioned that the Animus would resist his attempts to view further genetic memories and keep pulling Desmond back into the simulated island they were in – the designated compartment for Desmond’s consciousness. However, Clay said that he would help prevent the Animus from noticing him “wandering” into the outside partitions of his memory, just in case it concluded Desmond to be a virus and enacted a deletion. At one point, as Desmond worked to return to his body, Clay asked him if he could come with him, perhaps until he could find a body of his own.
As Desmond hesitantly declined, Clay admitted that he was not surprised, and that perhaps he had wasted his only chance. On another re-entrance to the island, Clay asked Desmond if he had ever regretted anything in his life. After Desmond admitted that he had wished he had been more patient with his parents, whom he had run away from, and that he wished things would have turned out different with Lucy, Clay simply thanked Desmond for making sense before vanishing again.
When Desmond had come close to completing the Synch Nexus, the Animus began to attempt to rectify the intrusions he had been causing in other memories. As it began to delete the Black Room and all of its contents, Clay grabbed onto Desmond and, in a final embrace in which he imprinted all of his genetic memories upon him, threw Desmond through the portal, saving his life.
Whether Clay Kaczmarek survived the deletion process by one mean or another, or not remains unknown. However, according to the “Security Breach Memo” in the Helix, it can be understood from a conversation between The Instruments of the First Will who hacked the Helix to communicate with Juno, and Juno herself, both Desmond and Clay are alive within “The Grey”.