Naomi Hunter is another one of the Metal Gear saga’s principal female characters-and arguably, one of it’s greatest (somewhat unsung) female heroes.
Naomi was orphaned at a young age during the Rhodesian civil war, and adopted as a sister by the soldier Frank Jaegar (Later the FOXHOUND agent Grey Fox), and later was helped by Big Boss to immigrate to the United States (Probably sometime after the Phantom Pain incident). However, her brother eventually got caught up in Big Boss’s vision of Outer Heaven (although he initially opposed it), and Solid Snake crippled both her guardians-Big Boss was put in a coma, and Grey Fox was maimed but still alive, rebuilt by Dr. Clark into the Cyborg Ninja. Naomi, curious about her birth parents (but unaware of Frank’s role in their deaths) became interested in genetics and nanotechnology.
She later put a plan for revenge into motion-first, against Dr. Clark, for using her brother as a Guinea pig, against Solid Snake, for crippling him in the first place. She freed Frank and killed Dr. Clark, and then joined the staff for the Shadow Moses mission, where she injected Solid Snake with nanomachines not only to track him, but carrying a strain of FOXDIE, a virus designed to target members of FOXHOUND and possibly Snake himself (although this was partially ordered to do this by Jim houseman). She also covered up certain details about her professions and pasts, but as the mission took some unexpected turns-including her brother’s appearance-the truth came out. However, she got to know Solid Snake personally-including his relationship with Big Boss and regretted what she’d done.
After the incident, she was jailed for a time, but was eventually released by Revolver Ocelot, whose persona had started to morph into that of Liquid Snake’s mental doppelganger. She then helped him develop a way to control the “Sons of the Patriots” system which controlled the world’s weapons and soldiers. Snake eventually rescued her in South America from Liquid, although she revealed that Snake’s system-due to a combination of FOXHOUND-including a new strain-and his own accelerated aging, was not only dying but could also mutate the FOXHOUND, potentially causing an epidemic with FOXHOUND targeting everyone!
After this rescue, she started a relationship on-board Snake’s plane the Nomad with Otacon (romantically) and a friendly relationship with his adopted daughter, Sunny Emmerich. Sunny-who was incredibly shy due to her isolation from the world to protect her-was able to break out of her shell a bit.
However, as always, Naomi had a hidden motive. She had developed a virus to essentially deactivate the Patriots-and gave the information to Sunny-a prodigy-to complete it. She later ‘rejoined’ Liquid, but this was a bit of a ruse as well. Eventually, she revealed to Otacon that she had in fact been dying from cancer, and had used nanomachines to suppress it in her system. At Shadow Moses she deactivated them and died-which greatly saddened Otacon.
However, Naomi’s legacy changed the world, when Snake used her computer virus on the Patriots-FOXALIVE-disabling them. She had recorded a farewell message to Snake and Otacon as well before her death.
Naomi : Snake… Hal. It’s you, isn’t it? I hope you’re listening. The virus you uploaded is using GW as a conduit to annihilate the entire AI network. It’s set to destroy all four AIs along with JD, the core that tied them all together. I’ve set this video to play back once they’re all gone. Sons of the Patriots was only the beginning. The Patriots were planning to use nanomachines to implement the System over the entire population. I had an obligation to stop it. With a little help from Sunny. She helped me… She believed her talents could help you all put GW to rest. What she created was an anti-AI FOXDIE. But this virus’s name is FOXALIVE. It’s… The conceptual opposite of the nanomachines that I created all those years ago. We wished to free the captured foxes… To let them run free in the wild. By the time you hear this, I’m afraid I’ll be gone. This is a strange feeling… Leaving a message to be delivered after you’ve died. Hal… If you’re listening…
Otacon : Naomi….
Naomi : I’m sorry… Sorry I deceived you. It hurt me more than anything else, lying to you like that. I wanted to apologize to you before… But I never got the chance.
Otacon : Naomi…. Naomi : And yet, in the end… You helped me feel the joy of living. Thank you, Hal. Thank you… Hal.
Otacon : Naomi….
Naomi : Snake… Hear me. Our country is an innocent child once more. A new dawn is rising. Now she can build a new destiny for herself. Snake… The time has come.
Naomi : You’ve earned your rest. The rose petal is about to fall…
Naomi also helped to revive the comatose Big Boss, for one last reunion with his son, in which he reassured Snake-via Naomi-that the new FOXDIE wouldn’t become an epidemic-although it was already too late for him.