@mirado:
The Battle Gear! You can't possibly tell me that we had all that build up for something that's reduced to filling a deployment mission checkbox. It was obviously cut, so why leave the other scenes in at all?
It was cut from gameplay due to balance issues. That's all KojiPro have said on that. I imagine they left it in because it still fills a purpose in Outer Ops.
Eli and the magical floating Metal Gear! I went and watched the cut episode 51, which is all well and good, but that stuff was cut for a reason. I don't know if that was time, or if the underlying idea was rejected, but as it stands, we have no canonical in-game resolution to that plot thread.
As it stands, we all know where Mantis and Liquid wind up... so why does it matter? In the True Ending events crawl that has accompanied every Metal Gear credits sequence since the first MGS, they explain quite clearly what happens to Liquid and Mantis. If you want further clarification I'll go find a screenshot of the crawl.
Quiet! She's gone, but she should also be barfing up larva right now. Hell, Venom should be barfing up larva right now as well, since the entire reason for her staying "Quiet" was to keep from unleashing the English plague on him. She gave a ton of instructions in English to the chopper, after all. And even if those few words weren't enough to activate the parasites and spread them to Snake, she's a walking bio-weapon (in more ways than one). They really just let that one go unresolved.
Quiet's mission was to gain Venom's trust and then when she was free to move around the base, she'd infect them. After seeing what kind of man he is, and what kind of place Diamond Dogs was, she has a change of heart. She realizes that her need for vengeance is kind of stupid, and that infecting the entire world with the English parasite, committing a holocaust that will kill untold millions (perhaps billions, depending on statistical data of exactly how many people in 1984 spoke English) is not worth the price of her revenge. There's also the subtext that Venom and Quiet are falling for each other, and I imagine that had something to do with her decision.
The catalyst for Quiet leaving was the epiphany that the English strain could mutate and become infectious anyway, even if she never spoke a word. She decides to leave Mother Base and Venom Snake behind and essentially goes on a suicide mission against the Soviet army in hopes of getting killed. If she dies, the parasite dies with her. Venom kind of fucks that plan up by performing a rescue operation, and so when she decides to finally speak in order to save his life, she realizes she's dooming herself. Skull Face supposes that you can get away with saying a few words here and there, but how much Quiet spoke definitely activated the parasite in her. She was a walking bio weapon, and that's why she leaves. She disappears into the Afghan desert to die, presumably by taking her own life. If you watch the ending to Mission 45 again, and pay attention to her face where she struggles to decide what to do, you can see the rollercoaster of emotions playing across her face. She understands what needs to happen now that the parasite has no doubt been activated, and she leaves Venom behind once she knows he'll be safe. She takes his walkman and records a goodbye.
It's not an unresolved plotpoint. It's all right there. The game doesn't explicitly tell you that she's going to kill herself, but it's heavily implied through visual cues, acting, and direction.
Miller's eyes! They were obviously playing that one up ("Did they do something to your eyes?" "It's just bright, that's all."), what with Code Talker's warning and the similarity to his eyes, amongst other references. Again, totally absent.
It's implied that he was infected with the parasite as well, but was given the Wallbachia treatment. That's the point of his eyes, I think. Subtle, sure, but it's there. A lot of the story in MGSV is told through the language of film, so it's pretty easy to see how someone might not pick up on everything that's being put down in this game. Not saying you're stupid for not getting it, because I imagine a lot of people aren't really familiar with what "film language" actually is.
Eli and Baby Mantis' red scarves! If you look on the shoulder of both Eli and Baby Mantis, they have the same red pieces of cloth in their epaulettes. Before the game came out, many speculated that this tied them together in some sort of unit. Given the fact that Mantis spent most of the game running around with Skull Face (and didn't meet Eli until the midway point), it seems odd that they'd share this feature.
I would have to go back and check, but I'm pretty sure Mantis's beret doesn't appear until the chopper scene where he discovers Eli. Even if that isn't the case, I imagine it could just be a bit of visual foreshadowing that is meant to subtly bind the two characters together, much in the same way that, from the moment you arrive in the ACC, you can zoom in on the chopper mirror and see the face of your avatar instead of Venom Snake.
Code Talker! I'd like to think he opened up a burger joint with Miller and spent the rest of his days chowing down, but, again, completely unresolved.
Code Talker is assumed to have spent his remaining days working on a way to restore his people to their romanticized glory. He's an old man to begin with (well over a century old), and I have to imagine he died at some point before Metal Gear or Metal Gear Solid. He was a bystander who was forced into this world through bad circumstances. It's not hard to say that when the whole affair is dealt with, he soon parts ways with Diamond Dogs and returns to his homeland in order to help the Dine.
Minor things! Why did Chico have a headphone jack implanted in his chest in GZ? Why did Huey insist on putting Hal in a Metal Gear? (Hell, how did Huey go from basically just Otacon in Peace Walker to ultra-scumbag here?) What happens to Sahelanthropus? Why does Kaz abandon his quest for vengeance against both Zero and Big Boss to go back to the US? He works under FOXHOUND before the Zanzibar Land disturbance, meaning he was both on Zero's territory and in Big Boss' unit.
Chico's headphone jack? No idea. It could be something to do with the parasites, but it's more than likely that he was just cruelly tortured. Huey put Hal in the Metal Gear because he's a fucked up piece of shit living in denial of the bad man that he is. A man who desires world peace does not create a nuclear weapon, he creates something to help heal the world in the wake of all the devastation human beings have caused. Think of it like this; Otacon realized what Metal Gear Rex was really for, was horrified, and ultimately founded Philanthropy as a way to atone for being used like he was. What is Huey's response to the Peace Walker incident? To build more terrifying mecha! A deadly parasite that can infect and kill millions if not billions of people? Why not subject it to testing and create an even deadlier strain! Huey is a scumbag because he can't hold himself accountable for the evil he's done. He cut a deal with Zero and the Patriots to go work for them after the Peace Walker incident. From the beginning in Peace Walker, Huey has been a contradiction. It was subtle as hell in Peace Walker, but it was still there.
Kaz abandons his quest for revenge once he realizes that it won't bring back everything they've lost. That's why he had such a hard on for murdering Skull Face and attempting to take down Cipher. It isn't until he realizes (or rather, is informed by Ocelot) that this whole thing is what Big Boss wanted. His closest friend left Kaz twisting in the wind. As for where Kaz winds up, it's explained in the post-credits conversation of the True Ending; he says essentially "fuck Big Boss, I'm going to take Venom and make him the man I always thought Big Boss was." He also vows to take care of Solid Snake and make him a better soldier than his old man in order to kill the bastard. Ocelot and Kaz essentially pick sides in that scene. Ocelot goes on to guide Liquid while Kaz goes on to guide Solid Snake.
He works in FOXHOUND because, like Big Boss, he doesn't want his enemy to see him coming. The best way to tackle your enemy isn't head on, it's sideways. Get out of their line of sight and they'll never see you coming. Kaz used Solid Snake as his proxy weapon to kill Big Boss, but in the meantime, he acted as though everything was fine between them. As for the connection with Cipher, he only wanted revenge on Cipher because he thought he was betrayed. He was playing both sides (although I think his true loyalty was to Big Boss; he says in Peace Walker that he was essentially working with Cipher in order to pump them for information), and he got burned. Kaz isn't a good guy. Nobody in MGSV is really a "good guy." Except for maybe Venom, as he turns out to be a better man than Big Boss. A man who chooses loyalty to his brothers in arms over loyalty to the mission.
Hopefully this gave you more answers than you found in the main game.
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