Free Will and Defiance (Cut Content, Part 2): An Aside Regarding Otacon
Until now [This section was originally placed after the discussion of the Gray Fox reveal – Austin], Metal Gear Solid has treated Snake and the player as a symbiotic entity, but in essence, the villains, unlike mission support are not aware of the player's presence. In reintroducing a character from his past, the game has taken the first steps in separating Snake from the player.
Otacon himself acts as a not just new surrogate for the audience, but actually a symbol of the player playing the game. For one, Otacon is based on a stereotype of the games likely target audience: he is a young man who likes anime and plays video games with a spine so weak he pisses his pants at the mere sight of Grey Fox. But that's not all. Over the course of the game, Otacon acts in more realistic and human ways than any of the other characters onscreen, as well as fits easily into his own stereotype. For example:
Otacon falls in love with Sniper Wolf. Kojima's artistic vision succeeded here in that most people remember Sniper Wolf for (what else) her death speech describing her traumatized past and such, allowing her to rise above what might have been her fate in any other game. It is thus: in any other game, Sniper Wolf would be a fanservice character, what with the femme fatalle personality and unzipped jacket with no bra. That Otacon falls in love with her is an indictment of audiences that would sexually idolize the character for her image alone despite both her obvious villainy and, on the other hand, her own humanity.
When Sniper Wolf dies, at one of the game's darkest and most honest moments, Otacon asks a very audience surrogate question in one of the more memorable exchanges in the game:
Otacon : Snake!! What was she fighting for? What am I fighting for!! What are you fighting for!?
Snake: If we make it through this, I'll tell you.
Otacon: Okay. I'll be searching too.
Otacon not only asks that question and receives the answer, but also interprets it, in the way an (intelligent) audience would.
In addition, the ways Otacon comes to help Snake highlight both the unreality of Snake's situation in their realness. When Otacon comes to help Snake when he's trapped in the prison cell, he's perfectly aware that he's incapable of incapacitating a guard, but he does what he can, bringing some ketchup because he thinks Snake might be hungry. ("Hungry? There aren't any hunger mechanics in this game. And I only eat food when I'm low on life! And I've never eaten ketchup to boost my health! What the fuck is going on here?!") Later, Snake, being a videogame character, is limited by system mechanics and user interface such that simply stacking crates in front of him prevents him from progressing, but of course Otacon does it no problem. When Snake asks how to freeze the PAL card, he replies ignorantly, "It's Alaska, go outside!" but when he realizes his mistake he notes how close Snake is to the freezer where he fought Raven.
The end effect on the game’s postmodern commentary on game structure is less itself a communication of theme and more itself an expression of structural intention: giving the game a character so much like the people most likely to be playing it (in positive and negative ways) simply helps to reinforce both that the player is not Snake, and also in many ways the impossibility of the game’s content itself. Otacon in MGS is possibly the most obvious commentary on form in the entire franchise.
The effect on the game’s political themes is also explicit: connecting Otacon, on a personal level, to the history of nuclear weapons and war, gives him a very specific end effect: his own arc is intended to reflect a sense of self-criticism for the player to undertake themselves, making them re-investigate how their role in a culture of violence helps persist that violence itself.
-Austin C. Howe, Maryland, 2013
 Also check out that specifically geeky way of defending her: "She loves dogs, she must be a good person!" The game is more sincere about that statement than it lets on, but it still comes off as, at best, naive on Otacon's part.
 I almost feel bad for putting this in a footnote but it's a detour: That is one of the best moments in the entire series. Just the sheer honesty of it is tragically beautiful, that in the haze of war, you take a moment to wonder why the hell everyone is shooting each other and you honestly have no idea. That this says multiple things on a thematic level is something else entirely. On one hand, it's Kojima putting in his typical pacifist word reminding you that war is pointless, on the other, he's readily admitting that to some degree, he's readily admitting that he's making this up as he goes along, which is itself genius as a reflection of how people justify their actions: "I'll do it now and figure out why I did later," or in the case of art, "I'll write this story and then give it a theme at the end," a stark indictment of how war stories are told (and similarly, game stories.)