Naomi Hunter

Dr. Naomi Hunter was the head of FOXHOUND's medical department prior the FOXHOUND Rebellion, and a member of Solid Snake's support team during that mission.

Early life
Naomi's parents were killed during the Rhodesian Civil War by Frank Jaeger, a FOXHOUND agent codenamed Gray Fox. Fox regretted this action, and subsequently adopted Naomi and raised her as a sister. Naomi never found out that Frank 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 1980, with the help of Big Boss, she would gain access to the United States to, later on, achieve her doctorate in genetics, specializing in nanotechnology-based gene therapy.

When Solid Snake defeated Big Boss and crippled Gray Fox, Naomi developed an intense hatred for him and vowed revenge. She obtained the identity of the real Dr. Naomi Hunter, who had gone missing in the Middle East some years prior.

In 2002, Naomi was recruited by the ATCG Company, a private pharmaceutical corporation that was jointly working with the Pentagon on a project to provide medical treatment to the Next-Generation Special Forces. In 2003, Naomi aided in Frank's escape from FOXHOUND's medical research division, by covering it up as a lab accident. She later became the head of FOXHOUND's medical staff and chief geneticist, and eventually joined the Pentagon's biological weapons program, perfecting the FOXDIE virus.

Naomi was on the team that was assembled to aid Solid Snake during the Shadow Moses incident. During Snake's briefing, she injected him with various nanomachines, nootropics and an anti-freezing peptide to prevent his blood and other bodily fluids from freezing. However, Naomi had also been ordered to infect Snake with the FOXDIE virus as part of his mission. Naomi, still seeking revenge, illegally modified the FOXDIE so that it would kill Snake in addition to Baker and FOXHOUND, but chose to set the virus to a "wildcard" value, leaving him vulnerable at a later time.

Naomi, after realizing that Snake was not a merciless killer as she had come to known him as, would eventually forgive Snake for nearly killing Frank following their cooperation in destroying Metal Gear REX; unaware of when the FOXDIE would kill Snake, Naomi told Snake to live his life to the fullest until it did. Although it was Frank's last wish for Naomi to know the truth behind her parents' death, Snake hid the truth.

Post-Shadow Moses
After Shadow Moses, Naomi was arrested for injecting Snake with FOXDIE, and placed in an undetermined maximum security facility. However, Nastasha Romanenko revealed in her book In the Darkness of Shadow Moses: The Unofficial Truth, that Naomi escaped from the facility with the aid of an unknown stranger. Romanenko adds that, "I know of only one person who could have breached the base's tight security and successfully led someone to freedom", suggesting that it was Solid Snake who freed her. Snake later revealed that he did not break her out, and Roy Campbell assumed it was probably Liquid Ocelot who really helped her escape.

In 2014, Naomi sends Otacon and Solid Snake a video message claiming to have been kidnapped by Liquid Ocelot in order to hijack the SOP System. In reality, she is working with him in order to destroy the Patriots' AI. Snake finds her in South America, and she discovers the cause of Snake's accelerated aging, as well as informing him that FOXDIE would cause an epidemic due to its genetic mutation. She also found the second strain of FOXDIE within him, which, unbeknownst to them, was injected by the Patriots via Drebin to kill EVA, Ocelot, and Big Boss. Naomi accompanies them to Eastern Europe. Aboard the Nomad she forms a bond with Sunny Gurlukovich, the daughter of Olga Gurlukovich, and becomes romantically involved with Otacon. She also tells Snake about the differences between his DNA and Liquids DNA when explaining the SOP's genetic locks, and also states that these same differences made FOXDIE unable to target Solid Snake, but infected Liquid Snake. She even felt a deep sympathy for Raiden, who became the next Cyborg Ninja, succeeding her foster brother and Sunny's mother. She creates 2/3 of the program that destroys GW and leaves the last part of the new program, FOXALIVE, to be finished by Sunny. She escapes the Nomad and returns to Liquid. After Vamp's death, she reveals she had been diagnosed with terminal cancer, kept in check through the use of nanomachines. She dies shortly afterward by suppressing said nanomachines.

In the debriefing, Naked Sin, it is revealed that she had been working with Ocelot and EVA, and that the three of them planned "Liquid's" uprising in advance. Naomi wanted to stop the Patriots and revive Big Boss, whom she loved along with Gray Fox. She left him a message telling about the plan, as well as the results of further research she did, explaining that the second strain of FOXDIE stopped the old strain from mutating, meaning Snake would not have to commit suicide.

Trivia

 * Naomi dies in the same place as her brother Gray Fox, in the hangar of Metal Gear REX.
 * Although she is said to have stolen the identity papers of "the real Naomi Hunter", at least "Hunter" is likely her real name, having obtained it from her brother.
 * Naomi gives a false history when questioned in Metal Gear Solid. She states that her Japanese Grandfather became assistant secretary to J. Edgar Hoover in The FBI and went undercover to bring down the Mafia in New York in the 1950's. Master Miller later revealed this was false as the J. Edgar Hoover was a well known racist which meant there were only white FBI agents in his time as director (1936–72) and the Mafia undercover operations first started in Chicago in 1960.
 * Although Naomi had a British accent in the original Metal Gear Solid, The Twin Snakes retconned the accent to sound more American. These altered accents remaining so in Metal Gear Solid 4. Mei Ling and Nastasha's accents were also retconned (Though it is unknown if Nastasha's Twin Snake's accent was canonically replaced or not, as she didn't appear at all in Metal Gear Solid 4).