JFK
From the Metal Gear Wiki
JFK was originally the name of another AI which was apparently heard speaking to Raiden, using the voices of Colonel Campbell and Rose, telling him to kill Solidus Snake.
Whereas its fellow AI, GW, seemed more intent on simply assisting Raiden in his mission, JFK seemed to be more intelligent and sentient, commenting on the human race in a seemingly condescending tone and explained the true nature of the S3 Plan. It also seemed to be working for The Patriots, as it told Raiden to kill Solidus.
The fate of JFK was not revealed and was never properly mentioned in Metal Gear Solid 2. It's name was provided in the original working script for the game, but is never explicitly mentioned in-game. In Metal Gear Solid 4, it is revealed that The Patriots had four AI's, none of which are called JFK, meaning this name is not the official name of the AI speaking to Raiden at the end of MGS2. The AI that was actually speaking to him could possibly be JD, but is not confirmed.
JFK takes its name from former United States President, John F. Kennedy, similar to how the four actual AI systems were named for four other presidents.
