Naomi killing herself because she has cancer, only for the game to reveal Sunny specifically programmed the Patriots AI so nanomachines could still be used for medical purposes (like counteracting cancer) even after the core was destroyed, was so much bullshit.
Hideo Kojima needs to not write stupid double-triple-quadruple agent plot twists if he’s just going have characters kill themselves for no reason so he doesn’t have to worry about following through on character development.
In my headcanon, Naomi didn’t die or kill herself. Her claim to cancer itself may even be a lie.
Naomi is a woman who you should never, ever take entirely at face value. In MGS1, she managed to trick her way onto Snake’s team to inject him with FOXDIE while assuming someone else’s identity. In MGS4, she “betrays” Snake, and regardless of how the player views it, in the MGS universe, she’s convincing enough that Snake and Otacon believed she really did betray them.
So here’s my thinking. Naomi faked her death because she wanted to be free from her past. Otacon abducted her and forced her to aid his agenda, despite her wanting nothing to do with it. She regrets putting FOXDIE in Snake’s system. She’s done things she regrets, and knows people will come for her to try to make her do the same thing or worse. Groups like World Marshal Inc or people like Senator Armstrong might abduct her, or try to coerce her by getting to Otacon or Sunny. Just having those connections puts her and the people around her at risk, which means she has to cut them to truly start over.
There’s no actual confirmation other than Naomi’s word that she ever had cancer. Pressing a syringe into her neck may have been dramatics, and Naomi acting like a bit of a drama queen may have been hamming it up… but it was effective enough for people not to consider that she may have faked her death.
From there, how or whether or not she escaped is kind of inconsequential, because anything can be made up. Maybe she snuck onto one of the ships. Maybe Otacon left one of the mechs with her under the idea she could use it to escape back to him if necessary, unaware she wasn’t actually helping him. Or, she really could have died, but had an escape plan ready if she had survived.
Personally, I’d been hoping we’d see Naomi return in a future Metal Gear Solid game, but sadly it looks like that’ll never happen now.