Subject X is described as an amnesiac girl around fifteen years old, who is found in Radiant Garden sometime during Terra-Xehanort's time as a researcher working under Ansem the Wise. At the time she cannot speak, and she is placed in a cell within the castle and investigated by the researchers who ask questions and run tests on her in an attempt to uncover her memory. She slowly regains patches of memory over time, describing her homeworld as like something from a "fairy tale", recalling "four friends and a key", and the words "May your heart be your guiding key".
She enjoys talking to Lea and Isa, two boys who often sneak into the castle to investigate the strange noises coming from within its walls. They plan to infiltrate the castle again one night and find a way to set her free.
Terra-Xehanort also takes particular interest in her, finding the tests to uncover her memory helping him to slowly recover his own. Operating behind his master's back, Terra-Xehanort wishes to perform a more dangerous experiment on her, claiming in a report that his previous test subjects were too weak and "suffered mental collapse".
Before he can do so however, Ansem the Wise learns of the inhumane experimentation his apprentices have been conducting and orders them to cease their research and release all of their subjects, including Subject X. Soon after, she is taken away from her cell by Braig. Finding themselves too late to help, Lea and Isa eventually decide to become apprentices of Ansem the Wise in order to find a lead on her. They would later continue into Organization XIII and scheme their way up its ranks for the same reason.
It is currently unknown what happened to Subject X after this, but at some point later she penned a report detailing her experience as a test subject, lamenting that "even now, years on," she has yet to recall her name and origin. She closes the report with "May my heart be my guiding key".
During the time period of Kingdom Hearts III, Ansem, Seeker of Darkness interrogates his former master Ansem the Wise for answers on the missing girl's whereabouts to no avail. Later, Saïx and Lea share a conversation reminiscing on their days as youths, reaffirming their decade-long goal of locating and helping her.