Anything that we as humans take even a little seriously is fodder for humor. Considering that the physical act of intercourse goes to the very root of our being as a biological imperative, it's one of the ripest topics for making jokes. That fruit hangs so low you can practically trip over it.
In this scene, we see Snake and Eva in the waterfall cave just following Snake's escape from Groznyj Grad. The full cutscene actually features a fairly touching sequence wherein the pair exchange a few suggestive comments and then kiss, but the romance goes right out the window in this bit. Discovering that Snake has a transmitter embedded in his body, Eva goes to great lengths to remove it from his body.
The cutscene is brilliant for a number of reasons. Kojima's use of the pair in shadows on the cave wall, so often used in film that it has become a cliché, gives him a license to get more than a little absurd with the events. Coupled with the grunting noises and innuendo so heavy you'd need a crane to lift it, it's just downright funny.
Another interesting aspect of the scene is that you can easily play the game and never encounter it, because its appearance is based on inaction. The transmitter on Snake's body is visible from the Cure Menu (the pause screen where Snake can perform first aid on himself) and can be removed at any time using a fork absconded from his cell at Groznyj Grad. If removed, Ocelot Unit soldiers who are looking for him will not appear out of the blue and attack, which is helpful. Of course, removing it means that this portion of the scene in the cave does not appear.
I wonder how many people missed out on seeing this as a result. I know from my personal experiences that I'm obsessive about healing any injury Snake has and it was probably only by accident (or an very lucky run through the jungle without taking much damage) that I had the good fortune to view it.
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