FOXDIE

FOXDIE is an engineered retrovirus developed by the DIA for the Pentagon. It is programmed to kill specific people by identifying the person's DNA and their nanomachines then causing cardiac arrest. The only known host for FOXDIE was Solid Snake.

Function
The FOXDIE virus enters macrophages in the target's bloodstream, then uses enzymes to attach to a DNA sequence that it has been "programmed" to recognize. Once the virus is attached to the DNA, the macrophage starts to produce the cytokine TNF (tumor necrosis factor) epsilon. The TNF-epsilon is carried along with the blood, to the heart, where it binds to the TNF receptors, causing the myocardial cells to die. This programmed cell death is called apoptosis, which leads to the victim suffering a heart attack. Natural heart attacks occur when the heart cells die from lack of oxygen and sugar, usually caused by a blocked coronary artery.

Origins
The development of the FOXDIE virus was one of the Pentagon's biological weapons programs. The FOXDIE program was led by the DIA operative Richard Ames under the authority of President George Sears, and under orders of the Patriots. The FOXDIE virus had been in development as the research hit a wall until 2003 when Dr. Naomi Hunter joined the project. Since then, the virus has been altered and re-created several times.

In 2005, the Pentagon had the U.S. Secretary of Defense Jim Houseman give the order for Naomi to inject the virus into an unaware Solid Snake shortly before he departed for Shadow Moses Island. The virus was programmed to kill off the ArmsTech President Kenneth Baker and the renegade members of FOXHOUND. The reason they injected the virus into Snake is so he could take down both the Sons of Big Boss and anyone else involved on Shadow Moses and at the same time the Pentagon would recover Metal Gear REX, the dummy warhead data, and the bodies of the Genome Soldiers intact. Baker was aware of FOXDIE's development as well as their plans with it, although he did not anticipate that the Pentagon would actually go through with it, and also attempted to warn Snake when he discovered it, but was unable to before drawing his last breath. Snake eventually discovered that Naomi had made an alteration to the virus so that at an unknown point in time it would also kill Snake, as an act of revenge for "killing" her closest relative: Frank Jaeger. When asked by Snake, regarding the amount of time he had until the virus killed him, Naomi replied, "Live, Snake. That's all I can say to you." Since Naomi had set the virus to activate at a "wildcard" value, she was unaware of when exactly he would die. However, it was later revealed that this FOXDIE wouldn't kill Snake, due to genetic variation inherent in the Les Enfants Terribles project, which differentiated his DNA code from that of Liquid Snake.

Post-Shadow Moses
Nastasha Romanenko received an optical disc, containing all the records of the personnel and research pertaining to the FOXDIE project, from her ex-husband Richard Ames. Ames willingly gave it to her in an attempt to keep her safe from the Patriots by using the disc's contents as leverage in case they tried to harm her. Shortly thereafter, she used the contents of the disc to explain the true events of the Shadow Moses Incident in a book called In the Darkness of Shadow Moses: The Unofficial Truth.

FOXDIE, as well as his infection of it from Naomi Hunter, was briefly mentioned by Snake during the Tanker Incident in 2007, when he stated that he was glad that while he is in Philanthropy, he won't have to worry about being given any "unwanted gifts." In 2009, a digital version of FOXDIE was uploaded into the GW AI of Arsenal Gear. Designed by Emma Emmerich to disrupt GW's operating system and render it unusable in case it fell into the wrong hands, it was altered just before the incident by the Patriots to delete any data about their "true" identities. The computer virus was part of the S3 Plan that manipulated the events of the Big Shell Incident into an orchestrated recreation of the Shadow Moses Incident.

Post-Big Shell
After the SOP-system was developed, it incorporated/inherited the nanomachine base for FOXDIE, namely as a strict genetic lock for the SOP system to prevent it from being hacked.

The biological FOXDIE that was still in Old 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 sequences and would begin to kill people at random, possibly becoming a worldwide pandemic. Snake learned of this after Naomi Hunter conducted medical tests on him in 2014.

It later became apparent, however, that Snake had previously been injected with a newer form of FOXDIE by Drebin during his failed mission to assassinate Liquid Ocelot in the Middle East, which halted the mutation of the original virus. The new FOXDIE was programmed by the Patriots to kill Big Mama, Liquid Ocelot and Big Boss. Although the new FOXDIE had uprooted the old, it would eventually mutate as well and become dangerous to the general population. However, this would not occur for several years, and would only live as long as Snake, which was an estimated year at best.

Victims of the old FOXDIE

 * Decoy Octopus
 * Kenneth Baker
 * Liquid Snake

Victims of the new FOXDIE

 * EVA
 * Revolver Ocelot
 * Big Boss

Behind the scenes
Naomi Hunter's character profile on the official Metal Gear Solid 4: Guns of the Patriots website, along with the Metal Gear Solid 4 Database, erroneously state that FOXDIE was created by the CIA. In Metal Gear Solid: The Twin Snakes, Revolver Ocelot claims that he survived the events on Shadow Moses due to the FOXDIE vaccine, in his phone call to Solidus Snake, though the Database states that it is unclear whether or not it ever actually existed. In addition, in Ocelot's call to Solidus for both Metal Gear Solid and its remake, Metal Gear Solid: The Twin Snakes, Ocelot explained that the vector (Solid Snake) was set to be activated soon, although whether this was meant to intend that they arranged for Naomi to edit FOXDIE or not is never elaborated on.

In Metal Gear Solid, FOXDIE was spelled "FoxDie." Subsequent games and sources spell it in capital letters.

When Big Boss explained that the true cause of deaths for Ocelot and EVA were in fact the new FOXDIE strand injected into Snake when explaining that he's been infected with it, a series of flashbacks also included Naomi among EVA and Ocelot. Whether this was intended to imply that Naomi was supposed to be one of FOXDIE's targets is unknown.