FoxDie is an engineered retrovirus developed by the Pentagon. It's programmed to kill specific people by identifying the person's DNA and their Nanomachines. Afterwards, it induces a cardiac arrest, killing the target.
The FoxDie virus goes into macrophages. After going into the macrophages, FoxDie uses enzymes to attach to the DNA sequence that it's "programmed" to recognize. Once the virus is attached to the specific DNA sequence, the macrophage starts to produce TNF (tumor necrosis factor) epsilon. TNF-epsilon is a cytokine that is carried along with the blood, to the heart. When TNF-epsilon reaches the heart, it binds to the TNF receptors, which cause certain pathways within the myocardial cell leading to its death. This programmed cell death is called apoptosis.
It's interesting to note that FoxDie causes a heart attack, but not like "normal" heart attacks. Normal heart attacks usually occur when a coronary artery is blocked, thus depriving the heart cells of oxygen and sugar, causing them to die. However, in both cases, heart cells die.
The project creating this virus was led by Richard Ames and in the authority of president George Sears. The Foxdie virus had been in development for years before the Shadow Moses incident, but research hit a wall until Naomi Hunter joined the project. Since then, the virus has been altered and re-created several times.
The virus was injected into an unaware Solid Snake shortly before he departed for Shadow Moses. The virus was programmed to kill off the President of ArmsTech, Kenneth Baker, and the renegade members of FOXHOUND. Interestingly, DARPA Chief Donald Anderson was not a part of FoxDie's programming due to the fact that Jim Houseman was good friends with him and wished to spare his life (although it was later revealed that he was also a founding member of The Patriots, so he was probably not coded into its programming for that reason as well). Snake also eventually discovered that Naomi made an unknown edit to the virus so that at some random point it would also kill Snake, because he "killed" her closest relative, Frank Jaeger. Dr. Hunter, when asked when Snake would die, said "Live, Snake. That's all I can say to you." Since Naomi had set the virus to activate at a "wildcard" value, it is unclear whether or not Dr. Hunter even knows when Snake will die. However, it's later revealed in Guns of the Patriots that this FOXDIE won't kill Snake due to unforeseen technicalities in Snake's DNA due to the Les Enfantes Terribles project (which also explain's Liquid's death from FOXDIE).
In 2009, the FoxDie virus was re-created into a computer virus by Emma Emmerich in order to disrupt the AI of Arsenal Gear (Codenamed GW) and subtract the parameters which The Patriots had setup in order to delete any data about them so that Solid Snake and Otacon would discover who they are. The computer virus was part of the S3 program test that manipulated the events of the Big Shell incident into an orchestrated recreation of the Shadow Moses incident.
The biological FoxDie that was still in Solid Snake began to mutate when his body started to age at an accelerated rate. This new FoxDie would eventually lose its ability to kill based on specific DNA and start killing people at random, and possibly go so far as to kill everyone on the planet. Although unknown to Snake, shortly before he learned this from Naomi, he was injected with a newer form of FoxDie (thanks to Drebin) which uprooted the mutated version. The new FoxDie was programmed by The Patriots to kill EVA, Ocelot and Big Boss. Although the new FoxDie uprooted the old, the new would, in the future, mutate as well. The new FoxDie would take the path of the old. However, it wouldn't happen for an untold number of years, and would only live as long as Solid Snake, which was an estimated year at best
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