Naomi is an orphan from Rhodesia whose parents were killed by Gray Fox during the Rhodesian Civil War. Gray Fox was unable to kill Naomi because she was just a kid. Feeling bad he then takes her with him so that he could take care of her. Naomi does not know her real family or name and considers Gray Fox to be her brother even though she knows they are not related by blood. Gray Fox told Solid Snake to tell Naomi about the truth. About how Gray Fox murdered her parents however, Solid Snake felt Naomi didn't need to know. She assumed the identity of "the real Naomi Hunter", who went missing in the Middle East. Big Boss later takes her to America, where she would study genetics in the hope that she can discover who she is by looking at her own DNA.
Naomi Hunter is played by Canadian-born voice actress Jennifer Hale in the English-speaking versions of the MGS series. Hiromi Tsuru played Naomi Hunter in the Japanese versions.
Metal Gear Solid
Naomi first appears in Metal Gear Solid as part of Snake's support staff. She serves as his medical adviser throughout the game and monitors his health through the nanomachines that she injected into Snakes body. However, it is later revealed she has a certain amount of anger towards Snake because he was responsible for killing her "benefactor" (Big Boss) and crippling Frank Jaeger (Gray Fox, who it turns out is her adopted brother). As a result Naomi, upon being ordered to inject the FOXDIE virus into Snake, intentionally modified it so the virus would eventually kill him, as well as making the time of his death random. In the end of MGS, she reveals she put aside her revenge and that FOXDIE will eventually kill Snake and since she programmed the virus value to a wild card or random number, even she doesn't know when he will die. Naomi also has an English accent in this game.
Metal Gear Solid 2
In MGS2 it is explained that Naomi was arrested after the events of MGS1 on Shadow Moses; she later escaped with the help of someone although it is not clear at that time who aided her escape.
Metal Gear Solid 4
In MGS4 we learn that it was Liquid Ocelot who helped her escape and he was in turn holding her captive, as he wanted to use her expertise in dealing with nanomachines in order to overthrow the SOP (Sons of the Patriots) system and to free the soldiers from the system. In his first trial in ACT 1 of MGS4, Liquid Ocelot and Naomi learn that they can't take soldiers off the system without causing them severe neurological damage and so decide instead to take over the system, a plan called "Guns of the Patriots". Snake rescues her from Ocelot's hold and in her stay with the protagonists, she becomes romantically involved with Otacon and friends with Sunny (she even shows her how to properly cook eggs!). However, she betrays the group and helps Ocelot in recovering Big Boss' body and activating GOP.
The group encounters her once again in Shadow Moses where she explains that she had to get close to the group so that she could give Sunny her prototype for FOXALIVE, the computer virus designed to destroy the Patriots' AI. She then reveals she was long ago diagnosed with cancer and has been using nano-machines to extend her life. She suppresses those nano-machines after Vamp is killed and dies in the hangar of Shadow Moses, just like Gray Fox. In the end it is revealed Naomi was working against Liquid Ocelot all along, similarly to how the Boss secretly worked against Volgin during Operation: Snake Eater, as part of her plan to put an end to both Outer Heaven and the Patriots. It is even hinted she was the one that convinced Big Boss to save Snake and kill Zero, thus renouncing Outer Heaven and "atoning for his sins."