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In October 2015, Elijah's mother brought her son to an Abstergo Industries clinic in New York City. The clinic was in fact a front allowing the Templars to collect DNA from the general population, at which point they discovered both his nature as a Sage and that he was the son of Desmond Miles. Not long after, the Instruments of the First Will also discoverd his true nature.
Later that year, in an effort to kidnap Elijah and bring him into Juno's cult, an Instruments agent named Richmond broke into their home and stabbed Elijah's mother to death in her kitchen. He then abducted the sleeping child from his bed.
Following his mother's death, Elijah remained with the Instruments, feigning his dedication, until late 2018 when he took the opportunity to eliminate Richard, his mother's killer, and flee with the Koh-i-Noor.