Naomi's parents were killed during the Rhodesian Civil War by Frank Jaeger. Jaeger deeply regretted this action, and subsequently adopted Naomi after finding her near the Zambezi River half-dead from starvation, raising her as a sister. She never found out that Jaeger was the man who had killed her parents.
Naomi never knew her true name, parents or ethnic origin; she became interested in genetics and nanotechnology in an effort to uncover this information. In the 1980s, with the help of Big Boss, whom she met during the Mozambican Civil War, she gained access to the United States, where she later achieved her doctorate in genetics, specializing in nanotechnology-based gene therapy.

After Solid Snake defeated Big Boss and crippled Jaeger (then known as Gray Fox) during the Zanzibar Land Disturbance, Naomi developed an intense hatred for him and vowed revenge. She obtained the identity of one Dr. Naomi Hunter, who had gone missing in the Middle East some years prior.

In 2002, Naomi was recruited by ATGC, a private pharmaceutical corporation that was jointly working with the Pentagon to develop gene therapy for the U.S. Army's Next-Generation Special Forces. During that year, Patriot founders EVA and Ocelot made contact with Naomi and enlisted her help to kill fellow founding member, Dr. Clark. In 2003, Naomi assisted her brother's escape from FOXHOUND's medical research division, after he killed Dr. Clark, covering it up as a lab accident and faking his death in the reports. She later became the head of FOXHOUND's medical staff and chief geneticist, eventually perfecting the Pentagon's FOXDIE virus. Unbeknownst to the Pentagon, however, Naomi completed the virus only to exact her revenge on Solid Snake.