Naomi Hunter's parents were a couple who conceived a daughter in the late 1970s. In 1979, they were killed by the mercenary Frank Jaeger in Rhodesia. After discovering the couple's daughter, Jaeger regretted his actions and decided to raise the girl as his sister. Taking the name Naomi Hunter, she would later speculate that she was of Indian descent, due to her skin tone.

During the Shadow Moses Incident in 2005, Jaeger revealed to Solid Snake that he killed Naomi's parents, and requested that the latter relay the truth to her. Following Jaeger's death, however, Snake withheld this information from her because Jaeger had been the only family that she ever knew.