From the Metal Gear Wiki

FOXDIE is a engineered Virus created to take out specific people by identifying the person's DNA and their Nanomachines. It 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, to do several different specific things.

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, the renegade members of FOXHOUND and the entire of the GENOME Army. 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. 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. Although the virus was successful in killing Liquid Snake, who was genetically identical to Solid Snake, Liquid's death served as indication that Solid Snake would eventually succumb to the virus. Dr. Naomi 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.

In 2009, the FOXDIE virus is 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.

[edit] Third Generation

In the year 2014, another version of FOXDIE had been developed, which Naomi refers to as it's "third generation". So far, intelligence seems to suggest that it can affect a select group or area of soldiers via the Nanomachines in their bloodstream, and their SOP system. No other information is available at this time.