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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The existence of rats and mice on the island, a non-native species to the islands, owe their presence to a combination of human intervention and their own resilience and adaptability, as they most likely were brought along as unknowing passengers aboard cargo ships. Likely the rat variety here is of the predominant genus known to this area as the Norway rat, which often has their introduction in this area as being attributed to survivors jumping off an 18th century Japanese shipwreck near Rat Island several hundred miles to the West. From there, they spread to other islands in the chain in a similar fashion. These rats are notorious for spreading bubonic plague (transmitted to man by the bite of a flea or other insect), endemic typhus fever, ratbite fever, and a few other volatile diseases.
Because they reproduce so quickly and destroy other native wildlife as well as the health concerns they pose, it is very necessary to put forth efforts to eradicate the pests wherever and whenever they are found. In a scene from the beginning of Metal Gear Solid, this is exactly what the personnel on Shadow Moses attempts to do by spraying rat poison in the ventilation ducts. Only after trying to explain the presence of rats on the island did it occur that this could be relevant to an angle in the storyline. As referenced by Liquid Snake, the Next Generation Special Forces which were enhanced by genetic manipulation were flawed due to the genetic symmetry, or similarity of their genes. He goes on saying, “We are all on the verge of death at the genetic level. We don’t know when or what type of disease will occur,” referring in this case to the propensity for all to be affected by the same deadly effects of disease. With these considerations in mind, it makes even more sense that they would take these precautions to protect themselves, even during an insurrection attempt.
The second time we experience the setting, the player is reintroduced with an intentional emphasis on nostalgia. During the approach to the base in Metal Gear Solid 4, a powerful mélange of music and visual cues culled from the first outing several years prior harps upon this fact. Drifting in and out in somewhat distorted and dreamlike sequences, snippets of old conversations with characters out of the series’ past, some now deceased, serve as powerful reminders of just how far the player has come to full circle. Knowing that some of those characters have been sacrificed in the journey back here can lend considerable strength to these reminisces. In addition to these, old security camera installations, the very same the player once avoided, break off the wall and fall to the ground useless while elsewhere electronically-controlled doors have also ceased to function. The base is unkempt with drifts of snow and heavy ice coating the surface of the empty heliport. In addition, new areas previously not accessible in the original Shadow Moses mission in 2005 are now accessible, namely the overland route to the Communications Tower, which was previously blocked by glaciers years before. Though we were not there to observe the gradual changes as they happened over time, the continuity seen between 
both games in reference to the environments presented amazes with its sense of an honest passage of time. Much like visiting an old hangout spot from childhood years after the fact, the player is easily captivated in discovering what has changed and what essentially has not. In one’s mind, a place once known has a tendency to remain that way as long as it is outside of their consciousness and will remain that way until reality interferes with this false assertion.
Indeed, a certain sense of sadness has been ascribed by many at this point in the game. No longer is Shadow Moses a memory at this point, but a metamorphosis has changed it into some new manifestation of itself, perhaps one not quite expected. It is at this part that the point being strived for has reached its intended poignancy and maturity. Just like Snake in MGS4, we are made all the more aware of just how much time has passed since then and are forced to face our mortality in the same way by recognizing how much older we are now. It is here that we simultaneously see the juxtaposition between not just what has changed about our memories over time, but also what has changed about one’s own self in the time that has passed. It is this same sense of a passage of time that is shared between real life and fiction that blurs the lines between the two and lends a special kind of ‘life’ to this particular fictional setting. Since all the aforementioned aspects lend a great amount of credit to the idea that Shadow Moses is essentially a feasible project - seeing it this way it’s not so hard to find yourself imagining that it is not such an impossibility for something like a ‘Shadow Moses’ to exist in our world. That is, if the right players were involved...
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