Clay Kaczmarek (1982 – 2012), also known as Subject 16 of the Animus Project, was a member of the Assassin Order during the early 21st century. Born into a family of engineers, Clay faced psychological problems due to developmental disorders and his father's neglectful attitude. Because of this, Clay ran into the Assassins while looking for acceptance.
As a member of the Assassin Brotherhood, Clay's most important mission was to infiltrate Abstergo Industries as a subject of the Animus Project, in order to obtain more information on the Animus. Labeled Subject 16, Clay was forced to relive the memories of his ancestors via his genetic memory.
When Clay found out that his teammate, Lucy Stillman—who infiltrated Abstergo years before and was tasked with getting Clay out of Abstergo safely—had abandoned their cause to join their enemies, the Templars, Clay had to spend days and hours of sessions inside the Animus.
Since it left his mind incapable of separating his own personality from those of his ancestors', Clay became mentally unstable to the point that he ultimately committed suicide.
After his death, Clay continued to exist as an AI recreation of his personality within the Animus. As such, he was able to manipulate much of the Animus' programming from within to help his successor in the Animus Project, Desmond Miles.
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.
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.
Eventually, Clay discovered 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. During one of these experiences, Clay found himself conversing with a figure calling herself Juno, who offered a shocking revelation about the true allegiances of his supposed ally, Lucy, as well as his own destiny.
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.
Life after death
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—hidden within twenty glyphs and ten rifts—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.
Following Clay's physical death, the Templars were left without the location of the Vatican Vault, though they had gained the knowledge that another Assassin, Altaïr Ibn-La'Ahad, had once seen a map projected by another Piece of Eden that could help them find it. Searching for a descendant of both Altaïr and Ezio Auditore, Abstergo happened upon Desmond Miles, who they swiftly kidnapped, and forced him into the Animus project, labeling him Subject 17.
By accessing private emails between Animus sessions, Desmond discovered one that Lucy had written to Dr. Vidic, detailing the Bleeding Effect, of which she explained how it was connected to Clay. She expressed her concern in pushing Desmond too hard; however, the e-mail was never replied to, and was evidently deleted by Vidic shortly after it was received.
Also, through the files unlocked in the glyphs Clay had created within the Animus, Desmond was able to learn many secrets about the Templar Order, both in the past and in his own time.
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 Empire,  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 American Civil War.
Personality and characteristics
Through his artificial construct, Clay was shown to be a sarcastic and witty man, usually speaking of his dire situation with cynical humor. Throughout his troubles with the Bleeding Effect, he proved driven to complete his mission, even as his sanity began to crumble; first to relay back Abstergo's plans for the Apple of Eden, then to pass on Juno's message.
Later on, as his perception of reality and identity began to falter and switch between past lives, he began speaking in riddles and cryptic clues. However, he kept his motivations to the end, even sacrificing his own life to reveal the Truth. Despite his own situation of being trapped in the Animus, as well as his occasional lapses of depression from his lost chances, Clay willingly helped Desmond regain his body and repair his subconscious; despite not being able to do so himself.
- Clay is a short form of the Old English name Clayton, claēg (clay) and tūn (town, settlement, village, enclosure): hence, "settlement near the clay pit." His surname, Kaczmarek, is a diminutive from the Old Polish version of the word karczmarz, meaning "innkeeper". His Polish surname may hint that he had Polish ancestry.
- The achievement entitled ".. .- -- .- .-.. .. ...- ." (Morse code for "I AM ALIVE") is earned by solving all Cluster puzzles. The achievement badge consists of the Morse code ".---- -....", which means "16".
- In the teaser trailer for Desmond's Journey, some coded text could be found, encrypted in Base64. One of these lines, preceded by the identifier S16, translated into: "08082012 I Am Not Alive" referring to the date of Clay's death.
- Due to the Black Room inverting the colors of Desmond's clothes, it's possible that it did the same to Clay, and that his appearance is not entirely accurate to what he wore in life.
- In volume 1 of the Les Deux Royaumes comics, Clay is referred to as "Michael". However, the graphic novel is not considered canon in that respect, as it directly contradicts the events of the games. In the English translations, he is correctly referred to by his first name. With this in mind, his introduction as "Michael" may be due to the comic's release prior to Assassin's Creed: Revelations.
- Writer Darby McDevitt stated Clay's madness was also induced by seeing too many alternate timelines or "Calculations" by the Isu, indicating this was the reason for why he said, "The sun, your son."
- Assassin's Creed (mentioned only)
- Assassin's Creed II (voice only)
- Assassin's Creed: Brotherhood (appears as a digital avatar)
- Assassin's Creed: Revelations
- Assassin's Creed Encyclopedia
- Assassin's Creed: Revelations – The Lost Archive – The End Is Only The Beginning
- Assassin's Creed: Revelations – The Lost Archive – The Order
- Assassin's Creed: Revelations – The Lost Archive – Abstergo
- Assassin's Creed: Revelations – The Lost Archive – The Truth
- Assassin's Creed: Revelations – The Lost Archive – Bleeding Effect
- Assassin's Creed: Revelations – The Lost Archive – The Mole
- Assassin's Creed: Revelations – The Lost Archive – The End of the Line
- Assassin's Creed: Revelations – Database: Subject 16
- Assassin's Creed II – Modern times
- Assassin's Creed: Brotherhood – Modern times
- Assassin's Creed: Revelations – Modern times
- Assassin's Creed IV: Black Flag – Subject 17 - memo 1
- Assassin's Creed – Modern times
- Assassin's Creed – Warren Vidic's email: "Subject No. 16"
- Assassin's Creed: Syndicate
- Assassin's Creed II – Paying Respects
- Assassin's Creed 1: Desmond
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