This article is by Metal Gear Confidential (careful, site seems to be infected) creator Mad Jackyl, who kindly emailed it to me and gave me permission to publish it. It's an honour to be able to present it here, and we thank him for giving more Metal Gear fans the opportunity to enjoy his insight.
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Author: Mad Jackyl
email: madjackyl16@yahoo.com
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By having Raiden log into nodes at different intervals to receive information, the Patriots' A.I. system could also in the same way keep tabs on him according to his login times and theoretically estimate his progress through Big Shell. With each node logged into, Raiden was effectively acting much as a messenger protein does within a biological organism (symbolized by Big Shell's structure this time) by spreading information between cells (or struts) and sharing information within the network. The difference being that Metal Gear Solid 2's "organism" - The Big Shell - was actually a controlled environment commandeered by the Patriots A.I. system to fulfill their ends.
To further make the case that Raiden can be viewed as a vector for the digital form of FoxDie, or information control as it may be more appropriately named, is that he is manipulated in not one, but two important yet intrinsically different ways. Firstly, he follows his orders like an automaton without questioning and quite unknowingly acts as a vector for information control. An example of this would be when he is instructed to rescue Emma Emmerich, whom he is told has the power to stop the A.I. system with a computer virus she holds. Instead, the Patriots' plan plays out perfectly. Raiden, acting as the Patriots' "carrier boy", as Ocelot so playfully alludes to, goes along with the effort to rescue Emma, who is lead to the computer terminal where the diskette is inserted. However, instead of deleting the A.I. system for good, the disk actually alters the information contained therein concerning the true identity of the Patriots! This is the first type of scenario in which Raiden is manipulated throughout the mission: unknowingly and unwillingly. G.W. goes haywire soon afterward from the buggy code inserted into the mainframe, which would seem to be a major setback to the Patriots' plan. However, this may have been a necessary and pre-planned turning point in the simulation. It changes the scenario slightly for Raiden as well in a subtle, yet important way. With G.W. operating at diminished capacity, the Patriots reveal their true allegiances- namely to themselves.
As explained by Ocelot, Arsenal Gear was propagated as being the perfectly defended sanctuary, thus making it that much more lucrative to the renegade Dead Cell, who would attempt to use the Patriots' own weapon to usurp them. In truth, it was entirely expendable - a virtual death trap for Dead Cell and the others who perished that held no real value other than to provide the perfect simulation grounds to stage the "S3" experiments. With his mission nearly complete and G.W. seeming to unravel by the minute, the next and final step in the S3 project is now set up for execution. When the Colonel and Rosemary begin acting erratically in their codec transmissions to Raiden, he uncovers the truth behind their identities when they reveal themselves as being a mere subset program of G.W. The ruse is up, or so it seems. Raiden now knows he had been manipulated throughout the entire mission, lied to by his so-called "trusted" superiors, who preyed upon his acceptance of them as paragons of truth based off of his perception of them, even though they had never once met. Seemingly delighted in the masquerade they had staged, the Patriots, still communicating via codec, then order Raiden to finish his mission by eliminating Solidus Snake, who has his own reasons for wanting Raiden dead. The two are still opposed to each other as before, however Raiden is now a knowing accomplice in his own manipulation. It serves as the ultimate test culminating in the final goal of the S3 plan: the Patriots knew from past experience that people could be controlled unwittingly by 
manipulation of the information presented to them. The real challenge was now to see if people could be controlled knowing full well that they were being manipulated all the while. The slaying of Solidus Snake by Raiden therefore, ultimately proved that this condition could in fact be met within an individual. And if one individual could be manipulated in such a manner, is there not reason to believe that the same model could be applied on a much larger scale? More likely than not, since, after all, Raiden did not choose whether or not to become an analog vector for information control any more than Snake chose to be a vector for FoxDie.
Once again, thank you to Mad Jackyl for this great analysis of the FOXDIE analogy in MGS2. As always, it's good to see a further breakdown of the layered narrative that MGS2 offers, and it really inspires me to think more about it myself. It really is an amazing game.
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