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- Big Boss falling in love with the Cardboard Box, and claiming that he feels at peace when he is inside of it, as if it was his destiny for him and the box to meet. What clinches it is Sigint's disbelief at Big Boss using the box as a means of camouflage and saying that he doesn't wanna know what he means when he says that he feels safe inside the box promptly ending the conversation. Furthermore this gives a hilarious insight into why Snake (and even Liquid likes the box according to Super Smash Brothers Brawl) likes the Cardboard Box so much, it runs in the family.
- The Food codec calls.
- At one point in the prologue, Snake sees a guard at the bridge. He looks up, notices a beehive up in the tree... and smirks.
- The second time you meet Ocelot, he pulls some of the fancy gun twirling he'll be known for, then twirls it into his holster. Then pulls it out and puts it back in the right way.
- The first time, Ocelot tries to kill you (because you're not The Boss), but jams his gun while showing off. Cue Naked Snake taking down every soldier nearby him using nothing but CQC and a tranquilizer gun. He then lectures Ocelot for showing off.
- Also during the second time, Ocelot takes EVA hostage but, thanks to a distraction from Snake-and his own lack of knowledge about revolvers-she evades him and backflips a motorcycle off his face. Snake lectures the guy again and he runs away with a tire tread mark on his face.
- Zero geeking out over Bond.
Zero: Maybe if you changed your name to Double-O Snake?
- Sigint talking about a nightmare he once had where a giant turd shot turds at everything and turned everything into turds.
- When Naked Snake asked if he could more or less make the first part of his codename true:
Naked Snake: So... can I take off my pants?
- Metal Gear Raiden: Snake Eraser.
(Raiden teleports in, Terminator-style, and gets knocked out of the way by Naked Snake)(Raiden teleports into the right time and place to stare at The Boss's Absolute Cleavage... and promptly gets bitch-slapped, while Snake stares in shock)
"You've created a time paradox! You can't go changing the future like that!"
(Raiden gets knocked into the air by a motorcycle, lands on top of Ocelot, who he kisses by accident)
"You've created a time paradox! Don't mess with the future! You have to understand the future!"
(Raiden gets *ahem*ed by Volgin)
"You can't do that! The future will be changed! You'll create a time paradox!"
- A certain radio conversation with SigInt, if you're wearing a Cardboard Box.
SigInt: Uh... Snake? What are you doing?
Naked Snake: I'm in a box.
SigInt: A cardboard box? Why are you...
Naked Snake: I dunno. I was just looking at it, and suddenly I got this irresistable urge to get inside! No, not an urge - more than that. It was my destiny to be here; In the box!
Naked Snake: Yeah. And then when I put it on, I suddenly got this feeling of inner peace. I can't put it into words. I feel... safe. Like this is where I was meant to be. Like I'd found the key to true happiness.
Naked Snake: Does any of that make sense?
SigInt: Not even a little.
Naked Snake: You should come inside the box... Then you'll know what I mean.
SigInt: Man, I don't wanna know what you mean! Between you and Para-Medic, is everyone but me that is hooked up with the Major strange!?
Naked Snake: ...
SigInt: Yeah, well, anyway, I suppose even that dumbass box might make a decent disguise if you wear it inside a building.
- Try the conversation about the glowing mushrooms.
Naked Snake: Para-Medic.
Para-Medic: What's up?
Naked Snake: You were right.
Para-Medic: About what?
Naked Snake: I ate a Russian glowcap and it charged up my batteries.
Naked Snake: What's wrong?
Para-Medic: I, uh... that's... that's great! Um, Snake, can you excuse me for a second?
Naked Snake: Sure.
(She leaves. Snake can still hear her.)
Para-Medic: Did you just hear that?
Sigint: Yeah. There's no way eating a bioluminescent mushroom would cause your batteries to recharge.
Para-Medic: What do you think it means?
Sigint: Beats me... maybe it's all in his mind.
Para-Medic: You mean like a placebo effect?
Sigint: Why not? You've seen how gullible he is.
Para-Medic: I guess there's no harm done. Should we let him keep believing it?
Sigint: Sounds good to me.
(She comes back)
Para-Medic: Okay, Snake, I'm back. Yes, the Russian glowcap is a glowing mushroom, so it'll recharge your batteries when you eat it.
- Talking to the people in your codec list (call Eva last) with the crocodile hat on shows you that the word "normal" does not apply to anyone involved with the FOX unit.
- The part when you rescue Sokolov. He follows Snake outside, imitating his MOVES, and somehow ending up with a Kamehame Hadoken gesture, at which point the camera pans over to Snake, staring at the scientist with a complete "What the frick are you doing?" look on his face.
- ALL the Easter Eggs in the third game qualify. Take your pick: between the conversation between Para-Medic and SigInt about Snake and the glowing mushrooms, calling Eva after you call everyone else with the crocodile head thing on, wear the scientist suit in the jungle, etc.
- MGS3 takes a lot of potshots at Raiden. One of the Codec conversations has Major Zero and Snake talk about the Raiden mask, it ends with them talking about the guy it's based on:
Naked Snake: What do I do if I meet that guy?
Major Zero: Beat the crap out of him.
- There's also this gem after you get Raikov's suit and call the Major.
Major Zero: Ah, your Raikov disguise has turned out nicely.
Naked Snake: Yeah. Not even his own mother could tell the difference.
Major Zero: Indeed. You're starting to irritate me already.
- The "Snake vs Monkey" minigame. Your only objective? Sneak up and capture the monkeys from Ape Escape.
- The trailer for the 3DS version features a cameo by... Yoshi. Yes, really.
- On New Game+, if the player calls The Boss when Snake is wearing the Tuxedo or GA-KO camo, the following conversation occurs:
Naked Snake: Looks pretty good on me, doesn't it?
The Boss: Are you out of your mind? You can't wear that in battle! It's like saying to the enemy, "Hey, here I am! Shoot me!"
Naked Snake: Well, I'll admit, it's a little on the flashy side...
The Boss: Then why don't you...
Naked Snake: But it does look good on me, doesn't it?
The Boss: ...
Naked Snake: You don't think so?
The Boss: Listen, wise ass! Camouflage isn't going to do jack if it doesn't help you blend in with your surroundings!
Naked Snake: Well, I think it looks good on me...
The Boss: (exasperated) Fine! Wear whatever you want!
Naked Snake: (in the most dejected tone of voice possible) ...I thought you'd like it...