Just something that I whipped up after seeing how a lot of people were disappointed in Naomi's pointless or contrived death (eg. why does her cancer kill her in 5 minutes?). Comments and criticisms are welcome.

--

(in Shadow Moses)

Hal: "What are you saying?"

Naomi: "Goodbye... Hal."

*Naomi reaches to inject herself but is stopped by someone's arm before she can do so.

The camera pans to Snake holding Naomi's arm, and the syringe, inches from her neck.*

Naomi: "Unh!"

Snake: "This doesn't have to end this way, Doctor."

Naomi: "No, it DOES have to end this way. Snake, I have to do this. I can't escape my fate."

Snake: "You told ME to choose, remember? We all have a choice."

Naomi: "I don't. I never have."

*Snake pauses for a beat.*

Snake: "Naomi... this isn't what Frank would have wanted."

*Naomi tries to push Snake away.*

Naomi: (crying) "What the hell do you know what he would have wanted?!"

Snake: "He loved you. He fought for you. He broke his own heart trying to protect you!"

Naomi: (surprised) "What?"

Snake: "He was the one who killed your parents. Out of guilt he adopted you as his sister. He never had the chance to tell you."

Naomi: (crying) "None of that matters now, Snake. Frank is dead. I should be too."

*Naomi tries to push the syringe into her neck, but Snake resists.*

Snake: (looking at the Mk-III) "Otacon, he loves you too."

*The Mk-III makes a little noise to acknowledge Snake's comment. Naomi glances at the Mk-III, then back at Snake.*

Naomi: "How can you forgive me after what I did to you?"

Snake: (looks down at his feet, pauses) "I have to make my own peace too."

Naomi: (wiping a tear from her face) "You don't understand, Snake... I'm no longer human. I can't be loved anymore. The nanomachines are all that stand between me and death."

Snake: (looks over at Raiden) "We can all find ways to be human."

*Several gekkos break through the walls of the room.*

Snake: (looks at no one in particular, as if not believing in what he is about to say) "To choose life over death."

*Raiden quickly looks away (flashback to Raiden and Rose in MGS2). Naomi hesitates for a few seconds, before handing the syringe over to Snake. The Mk-III makes another noise.*

*Several more gekkos drop from the ceiling.*

Raiden: "They're coming."

Naomi: "Let's go."

*Everybody runs toward the Metal Gear.*

Naomi: (onboard, wiping another tear from her face) "Snake, thank you."

Snake: (grunts) "You can thank me later. We still have work to do."

--

(At the briefing aboard the Missouri, Hal reveals all their mission data comes from Naomi, who is not present in the room. Hal reveals that Naomi and Sunny programmed FOXALIVE. Near the end of the briefing...)

Snake: "Anyone got a smoke?"

Meryl: "...Snake.."

Mei Ling: "Any OTHER questions?"

Meryl: "Can we trust her?"

Hal: "I do."

Meryl: (pauses) "What I mean is-"

Hal: "I know what you mean. Yes, we can. I've reviewed the code. FOXALIVE should be able to cut off Liquid's access by disabling GW and JD, but it will leave our infrastructure intact."

*Snake coughs.*

Mei Ling: "Then it's settled. We only have one chance at this. Good luck everyone."

*Everyone gets up and leaves except Hal and Snake.*

Hal: "You ever think about quitting, Snake?"

Snake: (grunts) "See you on the flight deck."

*Snake gets up to leave, his back facing Hal.*

Hal: "Snake, about Naomi -"

Snake: "Don't mention it."

Hal: "You saved her life, Snake."

Snake: (turns around to face Hal) "I don't save lives, Otacon. I'm just a killer."

Hal: (annoyed) "Stop saying that Snake, it isn't true. I don't know how many times you've saved me, or Meryl, or -"

Snake: (sarcastically) "You'd figure I'd be able to get in a smoke every now and again then, huh?"

Hal: (pauses) "Yeah."

Snake: "So you really think this FOXALIVE thing will work?"

Hal: (less assured than he was when the room was full) "I hope so. It's our only chance."

Snake: (grunts) "I've heard that before."

*Snake turns around and leaves the room. Hal sits down and sighs. A few moments later, Naomi walks in.*

Hal: (startled) "N-Naomi!"

Naomi: "Hal. I'm-"

*Hal reaches up to take off his glasses.*

Naomi: "No, leave them on."

Hal: "What?"

*Naomi places her hand on his and helps him put his glasses back on.*

Naomi: "I'm sorry, Hal, for everything."

Hal: "Huh?"

Naomi: "For betraying you, your trust. For lying to you. For using you..."

Hal: "Huh? Oh."

*There is an awkward silence.*

Hal: "It's OK, Naomi - "

Naomi: (crying) "No, it's not OK. Hal, I never wanted to hurt you. I never wanted to hurt Sunny..."

Hal: "But you're here now! That's all that matters!"

Naomi: "My brother broke his heart trying to protect me. I almost broke another heart today."

Hal: "Naomi... I.. I love you."

Naomi: (crying)

Hal: "What's wrong? Did I-"

Naomi: "No... Hal, if... when you and Snake are successful in taking down the AI, the nanomachines will cease to function... and I..."

Hal: "We'll fight it together. You won't be alone. You'll have Sunny, and me, and-"

Naomi: "I've been responsible for so much evil in this world, Hal. No matter what I do, I always end up hurting someone. I don't want to hurt you again..."

Hal: "No!" (Hal stands up)

Hal: (quieter) "No."

*Naomi looks startled, follows Hal with her eyes as he slowly walks away from her.*

Hal (with his back towards Naomi): "When I lost Sniper Wolf and Emma... I always regretted the time I spent with them. I... I was always one step too late. There when they died, but..."

*Naomi stands up.*

Naomi: "Hal-"

*Hal turns around to face Naomi.*

Hal: (decisively) "I won't be late this time, not with you."

*Naomi walks toward Hal slowly.*

Naomi: (stops crying, looks at Hal, wipes a tear off her face, smiles, more brightly) "Did I ever tell you you have beautiful eyes?"

Hal: "Huh?"

*Naomi moves in slowly and kisses Hal. They embrace. Fade to black.*

--

(At the wedding, after Hal's speech to Sunny)

*Hal is standing, looking off into the sun.*

Naomi: (brushes up to Hal, kisses him on the cheek, then places her head on his shoulder) "Mmm, the sun is beautiful, isn't it?"

Hal: (surprised) "Um, uh... oh. Yeah, it is."

Naomi: (with bittersweet contentment) "I wish every moment could be like this."

Hal: (tenses) "So do I."

Naomi: "What's wrong?"

Hal: (surprised that Naomi could read him) "Hmm? Oh. I-I'm letting Sunny out, to live outside."

Naomi: (looks up at Hal) "Yeah? Have you told Sunny yet?"

Hal: "Yeah."

Naomi: "What did she say?"

Hal: (pauses) "She's more worried about Snake... I am too."

Naomi: (looks off into the sun) "Snake..."

(progress to debriefing scene)