Exhibit A: Themes & Names
Metal Gear Solid 2 is about memes, or inherited information. It's about the dangers of the digital age, when technology has the ability to fool and control what people think and believe. It's about self-delusion too, and avoiding the truth. It's also about whether people are fit to decide what's "true".
With this in mind, it's obvious that the VR Theory is consistent with the themes of MGS2. As we established in the first part of this report, Kojima had the motive, means and opportunity to deceive the public through his own digital control...
(From Electronic Gaming Monthly, October 2001, Issue# 147:)
HK: I created the E3 trailer to give everyone an opportunity to imagine what the final game will be like. All rumors could be correct. All rumors could be wrong. One thing is for sure: I think I'll be able to fool and betray all of you in a pleasant way.
From this interview it's seems clear that Kojima underestimated the stubborness and expectations of his fanbase, since the betrayal was far from "pleasant" for most players. Perhaps if Kojima had known how extreme the criticism and resentment of his prank would have been, he wouldn't have added so much deception to the game. But judging by the final conversation with the Patriot AI it seems more likely that Kojima completely anticipated that some people would not be able to "handle the truth", and decided to reward those who could "get over" the fact that the mission was not real (in the sense that it wasn't the least bit genuine, at least,) and still search for valuable morals in the story. Because of this, it makes little thematic difference whether the events actually took place in the "real" Metal Gear world or simply in Raiden's head.
An examination of character names may seem anecdotal in regards to the VR Theory at first glance, but when considering the clear emphasis placed on the meaning of names in the Metal Gear world in general, and especially by the end of Sons of Liberty, where some people's names gain triple meanings. "Jack the Ripper", "Jack" from the Titanic movie, and the nickname for Japanese fighter jets during WWII... It is no stretch of the imagination to say that a lot of meaning has been packed into these names, and that they may contain hints about the true setting of the game...
E.E. / Emotion Engine
The first example of naming characters after computer technology is Emma Emmerich, who is usually referred to as "E.E." in the game. Kojima has officially said (although I can't find where) that she was named after the PlayStation 2's "Emotion Engine", which is also generally abbreviated to its intitials. This, if nothing else, proves that Kojima was drawing parallels between characters in the game and the larger interface itself.
Colonel / kernel
In computer science, the kernel is the central component of most computer operating systems (OS). Its responsibilities include managing the system's resources (the communication between hardware and software components). This fits perfectly with the role of the "Colonel" in the game, since he is the manifestation of Arsenal Gear's A.I., and that which communicates between it (the software) to Raiden/the player (the hardware).
Big Shell / shell
In computing, a shell is a piece of software that provides an interface for users. Typically, the term refers to an operating system shell which provides access to the services of a kernel. Kojima deliberately named the facility the "Big Shell" to allude to the fact that the whole structure is actually "a piece of software that provide an interface for users", providing "access to the services of a kernel"... Or, in this case a "Colonel".
Jack / jack
In electronics, a jack is generally a socket (female) connector, but because the related term "jack plug" is often abbreviated to just jack, confusion can easily arise. It's a physical component, through which data is transferred.
The character of Raiden, meanwhile, is how we "connect" to the Big Shell and the Colonel, and in a sense we see everything "through" him and his experiences. In order to access the Big Shell and the Colonel, we need to use a "Jack".
...Gender confusion, you say?
Rose / ROSE
The remote operations service element protocol (ROSE) is a sub-layer of application protocol that is part of the most basic programming network code. A network programming expert would probably be able to find some correlation between Rose's function in the game as a data analyst, and the function of the ROSE application protocol, but not me. However, even if the connection is weak, it is still possible that Kojima had something like this in mind when choosing her name.
Dead Cell / cell
A cell in the person of electronic design automation (EDA) is an abstract representation of a component within a schematic diagram or physical layout of an electronic circuit in software. A cell-based design methodology is a technique that enables designers to analyze chip designs at varying levels of abstraction. For example, one designer may focus on the logical function (high-level) and another may concentrate on physical implementation (low-level). The technique also enables designers to reuse components in more complex designs without understanding all of the implementation details.
We know that the name Dead Cell is inspired by the term "Red Cell" in US Military, but it could also refer to their function in the simulation Raiden is fighting in. Both the military and computer-design terms refer to something designed to "test" and "analyze" the effectiveness of something—in the US military it's their tactics and preparedness, and in the VR program it is the Patriot's ability to "generate and manipulate" our "persona, experiences, triumphs and defeats", as the Colonel explains. They're a fake unit, and whether it was "real life" or not, and their purpose was simply to test Raiden and generate his experiences.
With any of these "puns" or double entendres, it is possible to niggle and argue, dismissing them as coincidences, or, worse yet, trivial. It's highly likely that heavy thought was put into these names, and it wasn't simply to amuse the technologically-minded; it was to add evidence for those who bothered to look. To add plausibility to the dark suspicion of MGS2: the Plant Chapter was a computer simulation taking place in Raiden's head, and possibly the Tanker as well.
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Definitions taken from Wikipedia.org